From 60faa99ce2de7db242de65950ac86ffea1f61f24 Mon Sep 17 00:00:00 2001 From: George Chen <72078254+jiajic@users.noreply.github.com> Date: Thu, 5 Sep 2024 14:24:42 -0400 Subject: [PATCH] chore: code reorganization --- R/{vis_spatial.R => vis_spatial_gg.R} | 4144 ------------------------- R/vis_spatial_plotly.R | 4144 +++++++++++++++++++++++++ 2 files changed, 4144 insertions(+), 4144 deletions(-) rename R/{vis_spatial.R => vis_spatial_gg.R} (51%) create mode 100644 R/vis_spatial_plotly.R diff --git a/R/vis_spatial.R b/R/vis_spatial_gg.R similarity index 51% rename from R/vis_spatial.R rename to R/vis_spatial_gg.R index 888b35f..b3a6aca 100644 --- a/R/vis_spatial.R +++ b/R/vis_spatial_gg.R @@ -4487,4147 +4487,3 @@ spatDimCellPlot <- function(...) { - -# * #### -## 3-D plotly #### -## ----------- ## - -# ** dimension plot #### - - -#' @title .dimPlot_2d_plotly -#' @name .dimPlot_2d_plotly -#' @description Visualize cells at their 2D dimension reduction coordinates -#' with plotly -#' @returns plotly object -#' @keywords internal -.dimPlot_2d_plotly <- function(gobject, - spat_unit = NULL, - feat_type = NULL, - dim_reduction_to_use = "umap", - dim_reduction_name = "umap", - dim1_to_use = 1, - dim2_to_use = 2, - spat_enr_names = NULL, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = TRUE, - other_cell_color = "lightgrey", - other_point_size = 0.5, - show_NN_network = FALSE, - nn_network_to_use = "sNN", - network_name = "sNN.pca", - color_as_factor = TRUE, - cell_color = NULL, - cell_color_code = NULL, - show_cluster_center = FALSE, - show_center_label = TRUE, - center_point_size = 4, - label_size = 4, - edge_alpha = NULL, - point_size = 5) { - # Set feat_type and spat_unit - spat_unit <- set_default_spat_unit( - gobject = gobject, - spat_unit = spat_unit - ) - feat_type <- set_default_feat_type( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type - ) - - # data.table variables - cell_ID <- NULL - - ## dimension reduction ## - dim_dfr <- get_dimReduction( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - reduction = "cells", - reduction_method = dim_reduction_to_use, - name = dim_reduction_name, - output = "data.table" - ) - - dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use)] - dim_names <- colnames(dim_dfr) - dim_DT <- data.table::as.data.table(dim_dfr) - dim_DT[, "cell_ID" := rownames(dim_dfr)] - - - ## annotated cell metadata - cell_metadata <- combineMetadata( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spat_enr_names = spat_enr_names - ) - annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") - - - # create input for network - if (show_NN_network == TRUE) { - # nn_network - selected_nn_network <- get_NearestNetwork( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - nn_network_to_use = nn_network_to_use, - network_name = network_name, - output = "igraph" - ) - network_DT <- data.table::as.data.table(igraph::as_data_frame( - selected_nn_network, what = "edges")) - - # annotated network - old_dim_names <- dim_names - - annotated_network_DT <- merge(network_DT, dim_DT, by.x = "from", - by.y = "cell_ID") - from_dim_names <- paste0("from_", old_dim_names) - data.table::setnames(annotated_network_DT, old = old_dim_names, - new = from_dim_names) - - annotated_network_DT <- merge(annotated_network_DT, dim_DT, - by.x = "to", by.y = "cell_ID") - to_dim_names <- paste0("to_", old_dim_names) - data.table::setnames(annotated_network_DT, old = old_dim_names, - new = to_dim_names) - } - - - if (dim_reduction_to_use == "pca") { - pca_object <- get_dimReduction( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - reduction = "cells", - reduction_method = dim_reduction_to_use, - name = dim_reduction_name, - output = "dimObj" - ) - eigenvalues <- slot(pca_object, "misc")$eigenvalues - - if (!is.null(eigenvalues)) { - total <- sum(eigenvalues) - var_expl_vec <- (eigenvalues / total) * 100 - dim1_x_variance <- var_expl_vec[dim1_to_use] - dim2_y_variance <- var_expl_vec[dim2_to_use] - } - } - - - if (!is.null(select_cells) & !is.null(select_cell_groups)) { - if (is.null(cell_color)) { - stop("\n selection of cells is based on cell_color paramter, - which is a metadata column \n") - } - message("You have selected both individual cell IDs and a group - of cells") - group_cell_IDs <- annotated_DT[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - select_cells <- unique(c(select_cells, group_cell_IDs)) - } else if (!is.null(select_cell_groups)) { - select_cells <- annotated_DT[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - } - - - if (!is.null(select_cells)) { - annotated_DT_other <- annotated_DT[!annotated_DT$cell_ID %in% - select_cells] - annotated_DT_selected <- annotated_DT[annotated_DT$cell_ID %in% - select_cells] - - if (show_NN_network == TRUE) { - annotated_network_DT <- annotated_network_DT[ - annotated_network_DT$to %in% select_cells & - annotated_network_DT$from %in% select_cells] - } - - # if specific cells are selected - # annotated_DT = annotated_DT_selected - } - - - ## if no subsets are required - if (is.null(select_cells) & is.null(select_cell_groups)) { - annotated_DT_selected <- annotated_DT - annotated_DT_other <- NULL - } - - - ## annotated_DT_selected = all selected cells or all cells if no selection - ## annotated_DT_other = all not selected cells or NULL if no selection - - - pl <- plotly::plot_ly() - if (show_NN_network == TRUE) { - if (is.null(edge_alpha)) { - edge_alpha <- 0.5 - } else if (is.character(edge_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - edge_alpha <- 0.5 - } - - pl <- pl %>% plotly::add_segments( - name = network_name, - type = "scatter", - x = annotated_network_DT[[from_dim_names[1]]], - y = annotated_network_DT[[from_dim_names[2]]], - xend = annotated_network_DT[[to_dim_names[1]]], - yend = annotated_network_DT[[to_dim_names[2]]], - line = list( - color = "lightgray", - width = 0.5 - ), - opacity = edge_alpha - ) - } - - if (is.null(cell_color)) { - cell_color <- "lightblue" - pl <- pl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_selected[[dim_names[1]]], - y = annotated_DT_selected[[dim_names[2]]], - color = cell_color, - colors = cell_color, - marker = list(size = point_size) - ) - } else if (cell_color %in% colnames(annotated_DT_selected)) { - if (is.null(cell_color_code)) { - number_colors <- length(unique(annotated_DT[[cell_color]])) - cell_color_code <- set_default_color_discrete_cell( - instrs = instructions(gobject))(n = number_colors) - } - if (color_as_factor) { - annotated_DT_selected[[cell_color]] <- as.factor( - annotated_DT_selected[[cell_color]]) - } - - - pl <- pl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_selected[[dim_names[1]]], - y = annotated_DT_selected[[dim_names[2]]], - color = annotated_DT_selected[[cell_color]], - colors = cell_color_code, - legendgroup = annotated_DT_selected[[cell_color]], - marker = list(size = point_size) - ) - - if (!is.null(select_cells) & show_other_cells) { - pl <- pl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_other[[dim_names[1]]], - y = annotated_DT_other[[dim_names[2]]], - # legendgroup = annotated_DT[[cell_color]], - marker = list(size = other_point_size, - color = other_cell_color), - showlegend = FALSE - ) - } - - if (show_cluster_center == TRUE | show_center_label == TRUE) { - annotated_DT_centers <- annotated_DT_selected[, .( - center_1 = stats::median(get(dim_names[1])), - center_2 = stats::median(get(dim_names[2])) - ), - by = cell_color - ] - annotated_DT_centers[[cell_color]] <- as.factor( - annotated_DT_centers[[cell_color]]) - if (show_cluster_center == TRUE) { - pl <- pl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_centers[["center_1"]], - y = annotated_DT_centers[["center_2"]], - color = annotated_DT_centers[[cell_color]], - colors = cell_color_code, - legendgroup = annotated_DT_centers[[cell_color]], - marker = list(size = center_point_size, symbol = "x", - symbols = "x"), - showlegend = FALSE - ) - } - - if (show_center_label == TRUE) { - pl <- pl %>% - plotly::add_text( - x = annotated_DT_centers[["center_1"]], - y = annotated_DT_centers[["center_2"]], - type = "scatter", mode = "text", - text = annotated_DT_centers[[cell_color]], - textposition = "middle right", - textfont = list(color = "#000000", size = 16), - showlegend = FALSE - ) - } - } - } else { - stop("cell_color does not exist!\n") - } - - - - if (dim_reduction_to_use == "pca") { - if (!is.null(eigenvalues)) { - x_name <- paste0("pca", "-", dim_names[1]) - y_name <- paste0("pca", "-", dim_names[2]) - x_title <- sprintf("%s explains %.02f%% of variance", - x_name, var_expl_vec[1]) - y_title <- sprintf("%s explains %.02f%% of variance", y_name, - var_expl_vec[2]) - } - } else { - x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") - y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") - } - pl <- pl %>% plotly::layout( - xaxis = list(title = x_title), - yaxis = list(title = y_title), - legend = list(x = 100, y = 0.5, font = list(family = "sans-serif", - size = 12)) - ) - - return(pl) -} - - -#' @title .dimPlot_3d_plotly -#' @name .dimPlot_3d_plotly -#' @description Visualize cells at their 3D dimension reduction coordinates -#' with plotly -#' @returns plotly object -#' @keywords internal -.dimPlot_3d_plotly <- function(gobject, - spat_unit = NULL, - feat_type = NULL, - dim_reduction_to_use = "umap", - dim_reduction_name = "umap", - dim1_to_use = 1, - dim2_to_use = 2, - dim3_to_use = 3, - spat_enr_names = NULL, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = TRUE, - other_cell_color = "lightgrey", - other_point_size = 0.5, - show_NN_network = FALSE, - nn_network_to_use = "sNN", - network_name = "sNN.pca", - color_as_factor = TRUE, - cell_color = NULL, - cell_color_code = NULL, - show_cluster_center = FALSE, - show_center_label = TRUE, - center_point_size = 4, - label_size = 4, - edge_alpha = NULL, - point_size = 1) { - # Set feat_type and spat_unit - spat_unit <- set_default_spat_unit( - gobject = gobject, - spat_unit = spat_unit - ) - feat_type <- set_default_feat_type( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type - ) - - # data.table variables - cell_ID <- NULL - - ## dimension reduction ## - dim_dfr <- get_dimReduction( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - reduction = "cells", - reduction_method = dim_reduction_to_use, - name = dim_reduction_name, - output = "data.table" - ) - dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use, dim3_to_use)] - dim_names <- colnames(dim_dfr) - dim_DT <- data.table::as.data.table(dim_dfr) - dim_DT[, cell_ID := rownames(dim_dfr)] - - - ## annotated cell metadata - cell_metadata <- combineMetadata( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spat_enr_names = spat_enr_names - ) - annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") - - - # create input for network - if (show_NN_network == TRUE) { - # nn_network - selected_nn_network <- get_NearestNetwork( - gobject = gobject, spat_unit = spat_unit, - feat_type = feat_type, - nn_network_to_use = nn_network_to_use, - network_name = network_name, - output = "igraph" - ) - network_DT <- data.table::as.data.table(igraph::as_data_frame( - selected_nn_network, what = "edges")) - - # annotated network - old_dim_names <- dim_names - - annotated_network_DT <- merge(network_DT, dim_DT, by.x = "from", - by.y = "cell_ID") - from_dim_names <- paste0("from_", old_dim_names) - data.table::setnames(annotated_network_DT, old = old_dim_names, - new = from_dim_names) - - annotated_network_DT <- merge(annotated_network_DT, dim_DT, - by.x = "to", by.y = "cell_ID") - to_dim_names <- paste0("to_", old_dim_names) - data.table::setnames(annotated_network_DT, old = old_dim_names, - new = to_dim_names) - } - - if (dim_reduction_to_use == "pca") { - pca_object <- get_dimReduction( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - reduction = "cells", - reduction_method = dim_reduction_to_use, - name = dim_reduction_name, - output = "dimObj" - ) - - eigenvalues <- slot(pca_object, "misc")$eigenvalues - if (!is.null(eigenvalues)) { - total <- sum(eigenvalues) - var_expl_vec <- (eigenvalues / total) * 100 - dim1_x_variance <- var_expl_vec[dim1_to_use] - dim2_y_variance <- var_expl_vec[dim2_to_use] - } - } - - ## create subsets if needed - if (!is.null(select_cells) & !is.null(select_cell_groups)) { - if (is.null(cell_color)) { - stop("\n selection of cells is based on cell_color parameter, - which is a metadata column \n") - } - message("You have selected both individual cell IDs and a group of - cells") - group_cell_IDs <- annotated_DT[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - select_cells <- unique(c(select_cells, group_cell_IDs)) - } else if (!is.null(select_cell_groups)) { - select_cells <- annotated_DT[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - } - - if (!is.null(select_cells)) { - annotated_DT_other <- annotated_DT[!annotated_DT$cell_ID %in% - select_cells] - annotated_DT_selected <- annotated_DT[annotated_DT$cell_ID %in% - select_cells] - - if (show_NN_network == TRUE) { - annotated_network_DT <- annotated_network_DT[ - annotated_network_DT$to %in% select_cells & - annotated_network_DT$from %in% select_cells] - } - - # if specific cells are selected - annotated_DT <- annotated_DT_selected - } - - ## if no subsets are required - if (is.null(select_cells) & is.null(select_cell_groups)) { - annotated_DT_selected <- annotated_DT - annotated_DT_other <- NULL - } - - ## annotated_DT_selected = all selected cells or all cells if no selection - ## annotated_DT_other = all not selected cells or NULL if no selection - - - pl <- plotly::plot_ly() - if (is.null(cell_color)) { - cell_color <- "lightblue" - pl <- pl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_selected[[dim_names[1]]], - y = annotated_DT_selected[[dim_names[2]]], - z = annotated_DT_selected[[dim_names[3]]], - color = cell_color, - colors = cell_color, - marker = list(size = 2), - legendgroup = annotated_DT_selected[[cell_color]] - ) - } else { - if (cell_color %in% colnames(annotated_DT_selected)) { - if (is.null(cell_color_code)) { - number_colors <- length( - unique(annotated_DT_selected[[cell_color]])) - cell_color_code <- set_default_color_discrete_cell( - instrs = instructions(gobject))(n = number_colors) - } - if (color_as_factor) { - annotated_DT_selected[[cell_color]] <- as.factor( - annotated_DT_selected[[cell_color]]) - } - - pl <- pl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_selected[[dim_names[1]]], - y = annotated_DT_selected[[dim_names[2]]], - z = annotated_DT_selected[[dim_names[3]]], - color = annotated_DT_selected[[cell_color]], - colors = cell_color_code, - marker = list(size = point_size), - legendgroup = annotated_DT_selected[[cell_color]] - ) - - if (!is.null(select_cells) & show_other_cells) { - pl <- pl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_other[[dim_names[1]]], - y = annotated_DT_other[[dim_names[2]]], - z = annotated_DT_other[[dim_names[3]]], - # colors = other_cell_color, - marker = list(size = other_point_size, - color = other_cell_color), - showlegend = FALSE - ) - } - - - if (show_cluster_center == TRUE | show_center_label == TRUE) { - annotated_DT_centers <- annotated_DT_selected[, .( - center_1 = stats::median(get(dim_names[1])), - center_2 = stats::median(get(dim_names[2])), - center_3 = stats::median(get(dim_names[3])) - ), - by = cell_color - ] - annotated_DT_centers[[cell_color]] <- as.factor( - annotated_DT_centers[[cell_color]]) - if (show_cluster_center == TRUE) { - pl <- pl %>% plotly::add_trace( - mode = "markers", - type = "scatter3d", - data = annotated_DT_centers, - x = ~center_1, - y = ~center_2, - z = ~center_3, - color = annotated_DT_centers[[cell_color]], - colors = cell_color_code, - inherit = FALSE, - marker = list(size = 2, symbol = "x", symbols = "x"), - legendgroup = annotated_DT_centers[[cell_color]], - showlegend = FALSE - ) - } - if (show_center_label == TRUE) { - message(" center label is not clear to see in 3D plot\n You - can shut it down with show_center_label = FALSE") - pl <- pl %>% plotly::add_trace( - mode = "text", - type = "scatter3d", - data = annotated_DT_centers, - x = ~center_1, - y = ~center_2, - z = ~center_3, - text = annotated_DT_centers[[cell_color]], - legendgroup = annotated_DT_centers[[cell_color]], - inherit = FALSE, - showlegend = FALSE - ) - } - } - } else { - stop("cell_color does not exist!\n") - } - } - - if (show_NN_network) { - edges <- plotly_network( - annotated_network_DT, - "from_Dim.1", "from_Dim.2", "from_Dim.3", - "to_Dim.1", "to_Dim.2", "to_Dim.3" - ) - if (is.null(edge_alpha)) { - edge_alpha <- 0.5 - } else if (is.character(edge_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - edge_alpha <- 0.5 - } - - pl <- pl %>% plotly::add_trace( - name = network_name, - mode = "lines", - type = "scatter3d", - data = edges, - x = ~x, y = ~y, z = ~z, - inherit = FALSE, - line = list(color = "lightgray", width = 0.5), - opacity = edge_alpha - ) - } - - if (dim_reduction_to_use == "pca") { - if (!is.null(eigenvalues)) { - x_name <- paste0("pca", "-", dim_names[1]) - y_name <- paste0("pca", "-", dim_names[2]) - z_name <- paste0("pca", "-", dim_names[3]) - x_title <- sprintf("%s explains %.02f%% of variance", - x_name, var_expl_vec[1]) - y_title <- sprintf("%s explains %.02f%% of variance", - y_name, var_expl_vec[2]) - z_title <- sprintf("%s explains %.02f%% of variance", - z_name, var_expl_vec[3]) - } - } else { - x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") - y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") - z_title <- paste(dim_reduction_to_use, dim_names[3], sep = " ") - } - pl <- pl %>% plotly::layout( - scene = list( - xaxis = list(title = x_title), - yaxis = list(title = y_title), - zaxis = list(title = z_title) - ), - legend = list(x = 100, y = 0.5, - font = list(family = "sans-serif", size = 12)) - ) - return(pl) -} - - - - - - - -#' @rdname dimPlot -#' @returns plotly (dimplot3D only) -#' @export -dimPlot3D <- function(gobject, - spat_unit = NULL, - feat_type = NULL, - dim_reduction_to_use = "umap", - dim_reduction_name = "umap", - dim1_to_use = 1, - dim2_to_use = 2, - dim3_to_use = 3, - spat_enr_names = NULL, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = TRUE, - other_cell_color = "lightgrey", - other_point_size = 2, - show_NN_network = FALSE, - nn_network_to_use = "sNN", - network_name = "sNN.pca", - color_as_factor = TRUE, - cell_color = NULL, - cell_color_code = NULL, - show_cluster_center = FALSE, - show_center_label = TRUE, - center_point_size = 4, - label_size = 4, - edge_alpha = NULL, - point_size = 3, - show_plot = NULL, - return_plot = NULL, - save_plot = NULL, - save_param = list(), - default_save_name = "dim3D") { - if (is.null(dim3_to_use)) { - message("create 2D plot") - - pl <- .dimPlot_2d_plotly( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - dim_reduction_to_use = dim_reduction_to_use, - dim_reduction_name = dim_reduction_name, - dim1_to_use = dim1_to_use, - dim2_to_use = dim2_to_use, - spat_enr_names = spat_enr_names, - select_cell_groups = select_cell_groups, - select_cells = select_cells, - show_other_cells = show_other_cells, - other_cell_color = other_cell_color, - other_point_size = other_point_size, - show_NN_network = show_NN_network, - nn_network_to_use = nn_network_to_use, - network_name = network_name, - color_as_factor = color_as_factor, - cell_color = cell_color, - cell_color_code = cell_color_code, - show_cluster_center = show_cluster_center, - show_center_label = show_center_label, - center_point_size = center_point_size, - label_size = label_size, - edge_alpha = edge_alpha, - point_size = point_size - ) - } else { - message("create 3D plot") - pl <- .dimPlot_3d_plotly( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - dim_reduction_to_use = dim_reduction_to_use, - dim_reduction_name = dim_reduction_name, - dim1_to_use = dim1_to_use, - dim2_to_use = dim2_to_use, - dim3_to_use = dim3_to_use, - spat_enr_names = spat_enr_names, - select_cell_groups = select_cell_groups, - select_cells = select_cells, - show_other_cells = show_other_cells, - other_cell_color = other_cell_color, - other_point_size = other_point_size, - show_NN_network = show_NN_network, - nn_network_to_use = nn_network_to_use, - network_name = network_name, - color_as_factor = color_as_factor, - cell_color = cell_color, - cell_color_code = cell_color_code, - show_cluster_center = show_cluster_center, - show_center_label = show_center_label, - center_point_size = center_point_size, - label_size = label_size, - edge_alpha = edge_alpha, - point_size = point_size - ) - } - - - show_plot <- ifelse(is.null(show_plot), - readGiottoInstructions(gobject, param = "show_plot"), - show_plot) - save_plot <- ifelse(is.null(save_plot), - readGiottoInstructions(gobject, param = "save_plot"), - save_plot) - return_plot <- ifelse(is.null(return_plot), - readGiottoInstructions(gobject, param = "return_plot"), - return_plot) - - ## print plot - if (show_plot == TRUE) { - print(pl) - } - - ## save plot - if (save_plot == TRUE) { - do.call("all_plots_save_function", - c(list(gobject = gobject, plot_object = pl, - default_save_name = default_save_name), save_param)) - } - - ## return plot - if (return_plot == TRUE) { - return(pl) - } -} - - -#' @title plotUMAP_3D -#' @name plotUMAP_3D -#' @description Visualize cells according to dimension reduction coordinates -#' @param gobject giotto object -#' @param dim_reduction_name name of UMAP -#' @param default_save_name default save name of UMAP plot -#' @inheritDotParams dimPlot3D -gobject -dim_reduction_to_use -#' -dim_reduction_name -default_save_name -#' @details Description of parameters. -#' @family reduced dimension visualizations -#' @returns plotly -#' @examples -#' g <- GiottoData::loadGiottoMini("starmap") -#' plotUMAP_3D(g, dim_reduction_name = "3D_umap") -#' -#' @export -plotUMAP_3D <- function(gobject, - dim_reduction_name = "umap", - default_save_name = "UMAP_3D", - ...) { - dimPlot3D( - gobject = gobject, - dim_reduction_to_use = "umap", - dim_reduction_name = dim_reduction_name, - default_save_name = default_save_name, - ... - ) -} - - -#' @title plotTSNE_3D -#' @name plotTSNE_3D -#' @description Visualize cells according to dimension reduction coordinates -#' @param gobject giotto object -#' @param dim_reduction_name name of TSNE -#' @param default_save_name default save name of TSNE plot -#' @inheritDotParams dimPlot3D -gobject -dim_reduction_to_use -#' -dim_reduction_name -default_save_name -#' @details Description of parameters. -#' @family reduced dimension visualizations -#' @returns plotly -#' @examples -#' g <- GiottoData::loadGiottoMini("starmap") -#' plotTSNE_3D(g) -#' -#' @export -plotTSNE_3D <- function(gobject, - dim_reduction_name = "tsne", - default_save_name = "TSNE_3D", - ...) { - dimPlot3D( - gobject = gobject, - dim_reduction_to_use = "tsne", - dim_reduction_name = dim_reduction_name, - default_save_name = default_save_name, - ... - ) -} - - -#' @title plotPCA_3D -#' @name plotPCA_3D -#' @description Visualize cells according to 3D PCA dimension reduction -#' @param gobject giotto object -#' @param dim_reduction_name name of PCA -#' @param default_save_name default save name of PCA plot -#' @inheritDotParams dimPlot3D -gobject -dim_reduction_to_use -#' -dim_reduction_name -default_save_name -#' @details Description of parameters. -#' @family reduced dimension visualizations -#' @returns plotly -#' @examples -#' g <- GiottoData::loadGiottoMini("starmap") -#' plotPCA_3D(g) -#' -#' @export -plotPCA_3D <- function(gobject, - dim_reduction_name = "pca", - default_save_name = "PCA_3D", - ...) { - dimPlot3D( - gobject = gobject, - dim_reduction_to_use = "pca", - dim_reduction_name = dim_reduction_name, - default_save_name = default_save_name, - ... - ) -} - - - - - - -# ** #### -# ** spatial 3D plot #### - -#' @title .spatPlot_2d_plotly -#' @name .spatPlot_2d_plotly -#' @description Visualize cells at their 2D spatial locations with plotly -#' @returns plotly object -#' @keywords internal -.spatPlot_2d_plotly <- function(gobject, - spat_unit = NULL, - feat_type = NULL, - spat_loc_name = "raw", - sdimx = NULL, - sdimy = NULL, - spat_enr_names = NULL, - point_size = 3, - cell_color = NULL, - cell_color_code = NULL, - color_as_factor = TRUE, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = TRUE, - other_cell_color = "lightgrey", - other_point_size = 0.5, - show_network = FALSE, - spatial_network_name = "spatial_network", - network_color = "lightgray", - network_alpha = 1, - other_cell_alpha = 0.5, - show_grid = FALSE, - spatial_grid_name = "spatial_grid", - grid_color = NULL, - grid_alpha = 1, - show_legend = TRUE, - axis_scale = c("cube", "real", "custom"), - custom_ratio = NULL, - x_ticks = NULL, - y_ticks = NULL, - show_plot = FALSE) { - # Set feat_type and spat_unit - spat_unit <- set_default_spat_unit( - gobject = gobject, - spat_unit = spat_unit - ) - feat_type <- set_default_feat_type( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type - ) - - ## get spatial cell locations - cell_locations <- get_spatial_locations(gobject, - spat_unit = spat_unit, - spat_loc_name = spat_loc_name, - output = "data.table" - ) - if (is.null(cell_locations)) { - return(NULL) - } - - - ## extract spatial network - if (show_network == TRUE) { - spatial_network <- get_spatialNetwork(gobject, - spat_unit = spat_unit, - name = spatial_network_name, - output = "networkDT" - ) - } else { - spatial_network <- NULL - } - - ## extract spatial grid - if (show_grid == TRUE) { - spatial_grid <- get_spatialGrid(gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spatial_grid_name - ) - } else { - spatial_grid <- NULL - } - - ## get cell metadata - cell_metadata <- try( - expr = combineMetadata( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spat_loc_name = spat_loc_name, - spat_enr_names = spat_enr_names - ), - silent = TRUE - ) - - - if (inherits(cell_metadata, "try-error")) { - cell_locations_metadata <- cell_locations - } else if (nrow(cell_metadata) == 0) { - cell_locations_metadata <- cell_locations - } else { - cell_locations_metadata <- cell_metadata - } - - ## create subsets if needed - if (!is.null(select_cells) & !is.null(select_cell_groups)) { - message("You have selected both individual cell IDs and a group - of cells") - group_cell_IDs <- cell_locations_metadata[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - select_cells <- unique(c(select_cells, group_cell_IDs)) - } else if (!is.null(select_cell_groups)) { - select_cells <- cell_locations_metadata[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - } - - - if (!is.null(select_cells)) { - cell_locations_metadata_other <- cell_locations_metadata[ - !cell_locations_metadata$cell_ID %in% select_cells] - cell_locations_metadata_selected <- cell_locations_metadata[ - cell_locations_metadata$cell_ID %in% select_cells] - spatial_network <- spatial_network[spatial_network$to %in% - select_cells & spatial_network$from %in% - select_cells] - - # if specific cells are selected - # cell_locations_metadata = cell_locations_metadata_selected - } else if (is.null(select_cells)) { - cell_locations_metadata_selected <- cell_locations_metadata - cell_locations_metadata_other <- NULL - } - - - - ### set scale - axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) - - ### set ratio - ratio <- plotly_axis_scale_2D(cell_locations, - sdimx = sdimx, - sdimy = sdimy, - mode = axis_scale, - custom_ratio = custom_ratio - ) - - - - pl <- plotly::plot_ly() - - ## create network - if (show_network == TRUE) { - if (is.null(spatial_network)) { - stop("No usable spatial network specified! Please choose a - network with spatial_network_name=xxx") - } else { - if (is.null(network_alpha)) { - network_alpha <- 0.5 - } else if (is.character(network_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - network_alpha <- 0.5 - } - pl <- pl %>% plotly::add_segments( - name = spatial_network_name, - type = "scatter", - x = spatial_network[["sdimx_begin"]], - y = spatial_network[["sdimy_begin"]], - xend = spatial_network[["sdimx_end"]], - yend = spatial_network[["sdimy_end"]], - line = list( - color = network_color, - width = 0.5 - ), - opacity = network_alpha - ) - } - } - - ## create grid - if (show_grid == TRUE) { - if (is.null(spatial_grid)) { - stop("No usable spatial grid specified! Please choose a - network with spatial_grid_name=xxx") - } else { - if (is.null(grid_color)) { - grid_color <- "black" - } - edges <- plotly_grid(spatial_grid) - pl <- pl %>% plotly::add_segments( - name = "spatial_grid", - type = "scatter", - data = edges, - x = ~x, - y = ~y, - xend = ~x_end, - yend = ~y_end, - line = list( - color = grid_color, - width = 1 - ), - opacity = grid_alpha - ) - } - } - - - - if (!is.null(cell_color)) { - if (cell_color %in% colnames(cell_locations_metadata_selected)) { - if (is.null(cell_color_code)) { - number_colors <- length(unique( - cell_locations_metadata_selected[[cell_color]])) - cell_color_code <- set_default_color_discrete_cell( - instrs = instructions(gobject))(n = number_colors) - } - cell_locations_metadata_selected[[cell_color]] <- as.factor( - cell_locations_metadata_selected[[cell_color]]) - pl <- pl %>% plotly::add_trace( - type = "scatter", - mode = "markers", - x = cell_locations_metadata_selected[[sdimx]], - y = cell_locations_metadata_selected[[sdimy]], - color = cell_locations_metadata_selected[[cell_color]], - colors = cell_color_code, - marker = list(size = point_size) - ) - - - if (!is.null(select_cells) & show_other_cells) { - pl <- pl %>% plotly::add_trace( - type = "scatter", - mode = "markers", - data = cell_locations_metadata_other, - name = "unselected cells", - x = ~sdimx, - y = ~sdimy, - marker = list(size = other_point_size, - color = other_cell_color), - opacity = other_cell_alpha - ) - } - } else { - message("cell_color does not exist!") - } - } else { - pl <- pl %>% plotly::add_trace( - type = "scatter", - mode = "markers", - name = "selected cells", - x = cell_locations_metadata_selected[[sdimx]], - y = cell_locations_metadata_selected[[sdimy]], - colors = "lightblue", - marker = list(size = point_size) - ) - - if (!is.null(select_cells) & show_other_cells) { - pl <- pl %>% plotly::add_trace( - type = "scatter", - mode = "markers", - data = cell_locations_metadata_other, - name = "unselected cells", - x = ~sdimx, - y = ~sdimy, - marker = list( - size = other_point_size, - color = other_cell_color - ), - opacity = other_cell_alpha - ) - } - } - - - pl <- pl %>% - plotly::layout( - list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks) - ), - legend = list( - x = 100, y = 0.5, - font = list( - family = "sans-serif", - size = 12 - ) - ) - ) - - - return((pl)) -} - - - -#' @title .spatPlot_3d_plotly -#' @name .spatPlot_3d_plotly -#' @description Visualize cells at their 3D spatial locations with plotly -#' @returns plotly object -#' @keywords internal -.spatPlot_3d_plotly <- function(gobject, - spat_unit = NULL, - feat_type = NULL, - spat_loc_name = "raw", - sdimx = NULL, - sdimy = NULL, - sdimz = NULL, - spat_enr_names = NULL, - point_size = 3, - cell_color = NULL, - cell_color_code = NULL, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = TRUE, - other_cell_color = "lightgrey", - other_point_size = 0.5, - show_network = FALSE, - spatial_network_name = "spatial_network", - network_color = NULL, - network_alpha = 1, - other_cell_alpha = 0.5, - show_grid = FALSE, - spatial_grid_name = "spatial_grid", - title = "", - show_legend = TRUE, - axis_scale = c("cube", "real", "custom"), - custom_ratio = NULL, - x_ticks = NULL, - y_ticks = NULL, - z_ticks = NULL, - show_plot = FALSE) { - # Set feat_type and spat_unit - spat_unit <- set_default_spat_unit( - gobject = gobject, - spat_unit = spat_unit - ) - feat_type <- set_default_feat_type( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type - ) - - ## get spatial cell locations - cell_locations <- get_spatial_locations(gobject, - spat_unit = spat_unit, - spat_loc_name = spat_loc_name, - output = "data.table" - ) - if (is.null(cell_locations)) { - return(NULL) - } - - ## extract spatial network - if (show_network == TRUE) { - spatial_network <- get_spatialNetwork(gobject, - spat_unit = spat_unit, - name = spatial_network_name, - output = "networkDT" - ) - } else { - spatial_network <- NULL - } - - ## extract spatial grid - if (show_grid == TRUE) { - spatial_grid <- get_spatialGrid(gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spatial_grid_name - ) - } else { - spatial_grid <- NULL - } - - ## get cell metadata - cell_metadata <- try( - expr = combineMetadata( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spat_loc_name = spat_loc_name, - spat_enr_names = spat_enr_names - ), - silent = TRUE - ) - - - if (inherits(cell_metadata, "try-error")) { - cell_locations_metadata <- cell_locations - } else if (nrow(cell_metadata) == 0) { - cell_locations_metadata <- cell_locations - } else { - cell_locations_metadata <- cell_metadata - } - - - ## create subsets if needed - if (!is.null(select_cells) & !is.null(select_cell_groups)) { - message("You have selected both individual cell IDs and a group of - cells") - group_cell_IDs <- cell_locations_metadata[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - select_cells <- unique(c(select_cells, group_cell_IDs)) - } else if (!is.null(select_cell_groups)) { - select_cells <- cell_locations_metadata[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - } - - if (!is.null(select_cells)) { - cell_locations_metadata_other <- cell_locations_metadata[ - !cell_locations_metadata$cell_ID %in% select_cells] - cell_locations_metadata_selected <- cell_locations_metadata[ - cell_locations_metadata$cell_ID %in% select_cells] - spatial_network <- spatial_network[spatial_network$to %in% - select_cells & spatial_network$from %in% select_cells] - - # if specific cells are selected - # cell_locations_metadata = cell_locations_metadata_selected - } else if (is.null(select_cells)) { - cell_locations_metadata_selected <- cell_locations_metadata - cell_locations_metadata_other <- NULL - } - - - - ### set scale - axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) - - ### set ratio - ratio <- plotly_axis_scale_3D(cell_locations, - sdimx = sdimx, - sdimy = sdimy, - sdimz = sdimz, - mode = axis_scale, - custom_ratio = custom_ratio - ) - - - - pl <- plotly::plot_ly() - if (!is.null(cell_color)) { - if (cell_color %in% colnames(cell_locations_metadata_selected)) { - if (is.null(cell_color_code)) { - number_colors <- length(unique( - cell_locations_metadata_selected[[cell_color]])) - cell_color_code <- set_default_color_discrete_cell( - instrs = instructions(gobject))(n = number_colors) - } - cell_locations_metadata_selected[[cell_color]] <- as.factor( - cell_locations_metadata_selected[[cell_color]]) - pl <- pl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - data = cell_locations_metadata_selected, - x = ~sdimx, y = ~sdimy, z = ~sdimz, - color = cell_locations_metadata_selected[[cell_color]], - colors = cell_color_code, - marker = list(size = point_size) - ) - - - if (!is.null(select_cells) & show_other_cells) { - pl <- pl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - data = cell_locations_metadata_other, - name = "unselected cells", - x = ~sdimx, - y = ~sdimy, - z = ~sdimz, - marker = list( - size = other_point_size, - color = other_cell_color - ), - opacity = other_cell_alpha - ) - } - } else { - message("cell_color does not exist!") - } - } else { - pl <- pl %>% plotly::add_trace( - type = "scatter3d", - data = cell_locations_metadata_selected, - x = ~sdimx, - y = ~sdimy, - z = ~sdimz, - mode = "markers", - marker = list(size = point_size), - colors = "lightblue", name = "selected cells" - ) - - if (!is.null(select_cells) & show_other_cells) { - pl <- pl %>% plotly::add_trace( - type = "scatter3d", - mode = "markers", - data = cell_locations_metadata_other, - name = "unselected cells", - x = ~sdimx, y = ~sdimy, z = ~sdimz, - marker = list( - size = other_point_size, - color = other_cell_color - ), - opacity = other_cell_alpha - ) - } - } - - - ## plot spatial network - if (!is.null(spatial_network) & show_network == TRUE) { - if (is.null(network_color)) { - network_color <- "red" - } - edges <- plotly_network(spatial_network) - - pl <- pl %>% plotly::add_trace( - name = "sptial network", - mode = "lines", - type = "scatter3d", - data = edges, - x = ~x, - y = ~y, - z = ~z, - line = list(color = network_color, width = 0.5), - opacity = network_alpha - ) - } - - ## plot spatial grid - # 3D grid is not clear to view - - - pl <- pl %>% - plotly::layout( - scene = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - legend = list( - x = 100, y = 0.5, - font = list(family = "sans-serif", size = 12) - ) - ) - - - return(pl) -} - - - - - -#' @rdname spatPlot -#' @param sdimz z-axis dimension name (default = 'sdimy') -#' @param grid_alpha opacity of spatial grid -#' @param axis_scale the way to scale the axis -#' @param custom_ratio customize the scale of the plot -#' @param x_ticks set the number of ticks on the x-axis -#' @param y_ticks set the number of ticks on the y-axis -#' @param z_ticks set the number of ticks on the z-axis -#' @export -spatPlot3D <- function(gobject, - spat_unit = NULL, - feat_type = NULL, - sdimx = "sdimx", - sdimy = "sdimy", - sdimz = "sdimz", - spat_enr_names = NULL, - point_size = 3, - cell_color = NULL, - cell_color_code = NULL, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = TRUE, - other_cell_color = "lightgrey", - other_point_size = 0.5, - other_cell_alpha = 0.5, - show_network = FALSE, - spatial_network_name = "Delaunay_network", - network_color = NULL, - network_alpha = 1, - show_grid = FALSE, - spatial_grid_name = "spatial_grid", - grid_color = NULL, - grid_alpha = 1, - title = "", - show_legend = TRUE, - axis_scale = c("cube", "real", "custom"), - custom_ratio = NULL, - x_ticks = NULL, - y_ticks = NULL, - z_ticks = NULL, - show_plot = NULL, - return_plot = NULL, - save_plot = NULL, - save_param = list(), - default_save_name = "spat3D") { - if (is.null(sdimz)) { - message("create 2D plot") - - pl <- .spatPlot_2d_plotly( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - sdimx = sdimx, - sdimy = sdimy, - point_size = point_size, - cell_color = cell_color, - cell_color_code = cell_color_code, - select_cell_groups = select_cell_groups, - select_cells = select_cells, - show_other_cells = show_other_cells, - other_cell_color = other_cell_color, - other_point_size = other_point_size, - show_network = show_network, - network_color = network_color, - network_alpha = network_alpha, - other_cell_alpha = other_cell_alpha, - spatial_network_name = spatial_network_name, - show_grid = show_grid, - grid_color = grid_color, - grid_alpha = grid_alpha, - spatial_grid_name = spatial_grid_name, - show_legend = show_legend, - axis_scale = axis_scale, - custom_ratio = custom_ratio, - x_ticks = x_ticks, - y_ticks = y_ticks, - show_plot = FALSE - ) - } else { - message("create 3D plot") - pl <- .spatPlot_3d_plotly( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - sdimx = sdimx, - sdimy = sdimy, - sdimz = sdimz, - point_size = point_size, - cell_color = cell_color, - cell_color_code = cell_color_code, - select_cell_groups = select_cell_groups, - select_cells = select_cells, - show_other_cells = show_other_cells, - other_cell_color = other_cell_color, - other_point_size = other_point_size, - show_network = show_network, - network_color = network_color, - network_alpha = network_alpha, - other_cell_alpha = other_cell_alpha, - spatial_network_name = spatial_network_name, - spatial_grid_name = spatial_grid_name, - show_legend = show_legend, - axis_scale = axis_scale, - custom_ratio = custom_ratio, - x_ticks = x_ticks, - y_ticks = y_ticks, - z_ticks = z_ticks, - show_plot = FALSE - ) - } - - show_plot <- ifelse(is.null(show_plot), - readGiottoInstructions(gobject, param = "show_plot"), - show_plot) - save_plot <- ifelse(is.null(save_plot), - readGiottoInstructions(gobject, param = "save_plot"), - save_plot) - return_plot <- ifelse(is.null(return_plot), - readGiottoInstructions(gobject, param = "return_plot"), - return_plot) - - ## print plot - if (show_plot == TRUE) { - print(pl) - } - - ## save plot - if (save_plot == TRUE) { - do.call("all_plots_save_function", - c(list(gobject = gobject, plot_object = pl, - default_save_name = default_save_name), save_param)) - } - - ## return plot - if (return_plot == TRUE) { - return(pl) - } -} - - - - - - - - - -# ** #### -# ** spatial & dimension 3D plot #### - -#' @title spatDimPlot3D -#' @name spatDimPlot3D -#' @description Visualize cells according to spatial AND dimension -#' reduction coordinates in plotly mode -#' @inheritParams data_access_params -#' @inheritParams plot_output_params -#' @inheritParams plot_cell_params -#' @param plot_alignment direction to align plot -#' @param dim_reduction_to_use dimension reduction to use -#' @param dim_reduction_name dimension reduction name -#' @param dim1_to_use dimension to use on x-axis -#' @param dim2_to_use dimension to use on y-axis -#' @param dim3_to_use dimension to use on z-axis -#' -#' @param spat_loc_name name for spatial locations -#' @param sdimx = spatial dimension to use on x-axis -#' @param sdimy = spatial dimension to use on y-axis -#' @param sdimz = spatial dimension to use on z-axis -#' -#' @param spat_enr_names names of spatial enrichment results to include -#' @param show_NN_network show underlying NN network -#' @param nn_network_to_use type of NN network to use (kNN vs sNN) -#' @param network_name name of NN network to use, if show_NN_network = TRUE -#' @param show_cluster_center show the center of each cluster -#' @param show_center_label provide a label for each cluster -#' @param center_point_size size of the center point -#' @param label_size size of the center label -#' -#' @param select_cell_groups select subset of cells/clusters based on -#' cell_color parameter -#' @param select_cells select subset of cells based on cell IDs -#' @param show_other_cells display not selected cells -#' @param other_cell_color color of not selected cells -#' @param other_point_size size of not selected cells -#' -#' @param dim_point_size size of points in dim. reduction space -#' @param nn_network_color color of nn network -#' @param nn_network_alpha column to use for alpha of the edges -#' @param show_spatial_network show spatial network -#' @param spatial_network_name name of spatial network to use -#' @param spatial_network_color color of spatial network -#' -#' @param show_spatial_grid show spatial grid -#' @param spatial_grid_name name of spatial grid to use -#' @param spatial_grid_color color of spatial grid -#' @param spatial_grid_alpha alpha of spatial grid -#' @param spatial_point_size size of spatial points -#' @param spatial_network_color color of spatial network -#' @param spatial_network_alpha alpha of spatial network -#' -#' @param axis_scale the way to scale the axis -#' @param custom_ratio customize the scale of the plot -#' @param x_ticks set the number of ticks on the x-axis -#' @param y_ticks set the number of ticks on the y-axis -#' @param z_ticks set the number of ticks on the z-axis -#' @param legend_text_size size of legend -#' @returns plotly -#' @details Description of parameters. -#' @family spatial and dimension reduction visualizations -#' @export -spatDimPlot3D <- function(gobject, - spat_unit = NULL, - feat_type = NULL, - plot_alignment = c("horizontal", "vertical"), - dim_reduction_to_use = "umap", - dim_reduction_name = "umap", - dim1_to_use = 1, - dim2_to_use = 2, - dim3_to_use = 3, - spat_loc_name = NULL, - sdimx = "sdimx", - sdimy = "sdimy", - sdimz = "sdimz", - spat_enr_names = NULL, - show_NN_network = FALSE, - nn_network_to_use = "sNN", - network_name = "sNN.pca", - nn_network_color = "lightgray", - nn_network_alpha = 0.5, - show_cluster_center = FALSE, - show_center_label = TRUE, - center_point_size = 4, - label_size = 16, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = TRUE, - other_cell_color = "lightgrey", - other_point_size = 1.5, - cell_color = NULL, - color_as_factor = TRUE, - cell_color_code = NULL, - dim_point_size = 3, - show_spatial_network = FALSE, - spatial_network_name = "Delaunay_network", - spatial_network_color = "lightgray", - spatial_network_alpha = 0.5, - show_spatial_grid = FALSE, - spatial_grid_name = "spatial_grid", - spatial_grid_color = NULL, - spatial_grid_alpha = 0.5, - spatial_point_size = 3, - axis_scale = c("cube", "real", "custom"), - custom_ratio = NULL, - x_ticks = NULL, - y_ticks = NULL, - z_ticks = NULL, - legend_text_size = 12, - show_plot = NULL, - return_plot = NULL, - save_plot = NULL, - save_param = list(), - default_save_name = "spatDimPlot3D") { - # Set feat_type and spat_unit - spat_unit <- set_default_spat_unit( - gobject = gobject, - spat_unit = spat_unit - ) - feat_type <- set_default_feat_type( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type - ) - - # data.table variables - cell_ID <- NULL - - plot_alignment <- match.arg(plot_alignment, - choices = c("horizontal", "vertical")) - - # ********data prepare********# - ## dimension reduction ## - dim_dfr <- get_dimReduction( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - reduction = "cells", - reduction_method = dim_reduction_to_use, - name = dim_reduction_name, - output = "data.table" - ) - dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use, dim3_to_use)] - dim_names <- colnames(dim_dfr) - dim_DT <- data.table::as.data.table(dim_dfr) - dim_DT[, cell_ID := rownames(dim_dfr)] - - - ## annotated cell metadata - cell_metadata <- combineMetadata( - gobject = gobject, - feat_type = feat_type, - spat_unit = spat_unit, - spat_enr_names = spat_enr_names - ) - annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") - spatial_locations <- getSpatialLocations( - gobject, - spat_unit = spat_unit, - name = spat_loc_name, - output = "data.table" - ) - if (is.null(spatial_locations)) { - return(NULL) - } - - annotated_DT <- merge(annotated_DT, spatial_locations, by = "cell_ID") - - - if (dim_reduction_to_use == "pca") { - pca_object <- get_dimReduction( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - reduction = "cells", - reduction_method = dim_reduction_to_use, - name = dim_reduction_name, - output = "dimObj" - ) - eigenvalues <- slot(pca_object, "misc")$eigenvalues - - if (!is.null(eigenvalues)) { - total <- sum(eigenvalues) - var_expl_vec <- (eigenvalues / total) * 100 - dim1_x_variance <- var_expl_vec[dim1_to_use] - dim2_y_variance <- var_expl_vec[dim2_to_use] - if (!is.null(dim3_to_use)) { - dim3_z_variance <- var_expl_vec[3] - } - } - } - - - - ## nn network - if (show_NN_network) { - # nn_network - selected_nn_network <- get_NearestNetwork( - gobject = gobject, - feat_type = feat_type, - spat_unit = spat_unit, - nn_network_to_use = nn_network_to_use, - network_name = network_name, - output = "igraph" - ) - network_DT <- data.table::as.data.table(igraph::as_data_frame( - selected_nn_network, what = "edges")) - - # annotated network - old_dim_names <- dim_names - - annotated_network_DT <- merge(network_DT, dim_DT, by.x = "from", - by.y = "cell_ID") - from_dim_names <- paste0("from_", old_dim_names) - data.table::setnames(annotated_network_DT, old = old_dim_names, - new = from_dim_names) - - annotated_network_DT <- merge(annotated_network_DT, dim_DT, - by.x = "to", by.y = "cell_ID") - to_dim_names <- paste0("to_", old_dim_names) - data.table::setnames(annotated_network_DT, old = old_dim_names, - new = to_dim_names) - } - - - - - ## extract spatial network - if (show_spatial_network == TRUE) { - spatial_network <- get_spatialNetwork(gobject, - spat_unit = spat_unit, - name = spatial_network_name, - output = "networkDT" - ) - } else { - spatial_network <- NULL - } - - - ## extract spatial grid - if (show_spatial_grid == TRUE) { - spatial_grid <- get_spatialGrid(gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spatial_grid_name - ) - } else { - spatial_grid <- NULL - } - - - # create matching cell_color_code - if (is.null(cell_color_code)) { - if (is.character(cell_color)) { - cell_metadata <- pDataDT(gobject, - feat_type = feat_type, - spat_unit = spat_unit - ) - if (cell_color %in% colnames(cell_metadata)) { - if (color_as_factor == TRUE) { - number_colors <- length(unique(cell_metadata[[cell_color]])) - cell_color_code <- set_default_color_discrete_cell( - instrs = instructions(gobject))(n = number_colors) - names(cell_color_code) <- unique( - cell_metadata[[cell_color]]) - } - } - } - } - - - ## subset cell selection ## - if (!is.null(select_cells) & !is.null(select_cell_groups)) { - if (is.null(cell_color)) { - stop("\n selection of cells is based on cell_color paramter, - which is a metadata column \n") - } - message("You have selected both individual cell IDs and a group - of cells") - group_cell_IDs <- annotated_DT[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - select_cells <- unique(c(select_cells, group_cell_IDs)) - } else if (!is.null(select_cell_groups)) { - select_cells <- annotated_DT[get(cell_color) %in% - select_cell_groups][["cell_ID"]] - } - - - if (!is.null(select_cells)) { - annotated_DT_other <- annotated_DT[!annotated_DT$cell_ID %in% - select_cells] - annotated_DT_selected <- annotated_DT[annotated_DT$cell_ID %in% - select_cells] - - if (show_NN_network == TRUE) { - annotated_network_DT <- annotated_network_DT[ - annotated_network_DT$to %in% select_cells & - annotated_network_DT$from %in% select_cells] - } - if (show_spatial_network == TRUE) { - spatial_network <- spatial_network[spatial_network$to %in% - select_cells & - spatial_network$from %in% - select_cells] - } - - # if specific cells are selected - # annotated_DT = annotated_DT_selected - } - - - ## if no subsets are required - if (is.null(select_cells) & is.null(select_cell_groups)) { - annotated_DT_selected <- annotated_DT - annotated_DT_other <- NULL - } - - ## annotated_DT_selected = all selected cells or all cells if no selection - ## annotated_DT_other = all not selected cells or NULL if no selection - - - - ########### dim plot ########### - # 2D plot - if (is.null(dim3_to_use)) { - dpl <- plotly::plot_ly() - if (show_NN_network == TRUE) { - if (is.null(nn_network_alpha)) { - nn_network_alpha <- 0.5 - } else if (is.character(nn_network_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - nn_network_alpha <- 0.5 - } - dpl <- dpl %>% plotly::add_segments( - name = network_name, - type = "scatter", - x = annotated_network_DT[[from_dim_names[1]]], - y = annotated_network_DT[[from_dim_names[2]]], - xend = annotated_network_DT[[to_dim_names[1]]], - yend = annotated_network_DT[[to_dim_names[2]]], - line = list( - color = nn_network_color, - width = 0.5 - ), - opacity = nn_network_alpha - ) - } - - if (is.null(cell_color)) { - # cell_color = "lightblue" - dpl <- dpl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_selected[[dim_names[1]]], - y = annotated_DT_selected[[dim_names[2]]], - # color = "lightblue", - # colors ="lightblue", - marker = list( - size = dim_point_size, - color = "lightblue" - ), - showlegend = FALSE - ) - } else if (cell_color %in% colnames(annotated_DT_selected)) { - if (color_as_factor) { - annotated_DT_selected[[cell_color]] <- as.factor( - annotated_DT_selected[[cell_color]]) - } - - - dpl <- dpl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_selected[[dim_names[1]]], - y = annotated_DT_selected[[dim_names[2]]], - color = annotated_DT_selected[[cell_color]], - colors = cell_color_code, - legendgroup = annotated_DT_selected[[cell_color]], - marker = list(size = dim_point_size) - ) - } else { - stop("cell_color does not exist!\n") - } - - - if ((show_cluster_center == TRUE | show_center_label == TRUE) & - !is.null(cell_color)) { - annotated_DT_centers <- annotated_DT_selected[, .( - center_1 = stats::median(get(dim_names[1])), - center_2 = stats::median(get(dim_names[2])) - ), - by = cell_color - ] - annotated_DT_centers[[cell_color]] <- as.factor( - annotated_DT_centers[[cell_color]]) - if (show_cluster_center == TRUE) { - dpl <- dpl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_centers[["center_1"]], - y = annotated_DT_centers[["center_2"]], - color = annotated_DT_centers[[cell_color]], - colors = cell_color_code, - legendgroup = annotated_DT_centers[[cell_color]], - marker = list(size = center_point_size, symbol = "x", - symbols = "x"), - showlegend = FALSE - ) - } - - if (show_center_label == TRUE) { - dpl <- dpl %>% plotly::add_text( - x = annotated_DT_centers[["center_1"]], - y = annotated_DT_centers[["center_2"]], - type = "scatter", mode = "text", - text = annotated_DT_centers[[cell_color]], - textposition = "middle right", - textfont = list( - color = "#000000", - size = label_size - ), - showlegend = FALSE - ) - } - } - if (show_other_cells == TRUE) { - dpl <- dpl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_other[[dim_names[1]]], - y = annotated_DT_other[[dim_names[2]]], - marker = list(size = other_point_size, - color = other_cell_color), - showlegend = FALSE - ) - } - if (dim_reduction_to_use == "pca") { - if (!is.null(eigenvalues)) { - x_name <- paste0("pca", "-", dim_names[1]) - y_name <- paste0("pca", "-", dim_names[2]) - x_title <- sprintf("%s explains %.02f%% of variance", - x_name, var_expl_vec[1]) - y_title <- sprintf("%s explains %.02f%% of variance", - y_name, var_expl_vec[2]) - } - } else { - x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") - y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") - } - dpl <- dpl %>% plotly::layout( - xaxis = list(title = x_title), - yaxis = list(title = y_title), - legend = list(x = 100, y = 0.5, - font = list(family = "sans-serif", - size = legend_text_size)) - ) - } - # 3D plot - else if (!is.null(dim3_to_use)) { - dpl <- plotly::plot_ly(scene = "scene1") - if (is.null(cell_color)) { - # cell_color = "lightblue" - dpl <- dpl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_selected[[dim_names[1]]], - y = annotated_DT_selected[[dim_names[2]]], - z = annotated_DT_selected[[dim_names[3]]], - color = "lightblue", - colors = "lightblue", - marker = list(size = dim_point_size), - showlegend = FALSE - ) - # legendgroup = annotated_DT_selected[[cell_color]]) - } else { - if (cell_color %in% colnames(annotated_DT_selected)) { - if (is.null(cell_color_code)) { - number_colors <- length(unique( - annotated_DT_selected[[cell_color]])) - cell_color_code <- set_default_color_discrete_cell( - instrs = instructions(gobject) - )(n = number_colors) - } - if (color_as_factor) { - annotated_DT_selected[[cell_color]] <- as.factor( - annotated_DT_selected[[cell_color]]) - } - dpl <- dpl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_selected[[dim_names[1]]], - y = annotated_DT_selected[[dim_names[2]]], - z = annotated_DT_selected[[dim_names[3]]], - color = annotated_DT_selected[[cell_color]], - colors = cell_color_code, - marker = list(size = dim_point_size), - legendgroup = annotated_DT_selected[[cell_color]] - ) - } else { - stop("cell_color does not exist!\n") - } - } - if (show_other_cells == TRUE) { - dpl <- dpl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_other[[dim_names[1]]], - y = annotated_DT_other[[dim_names[2]]], - z = annotated_DT_other[[dim_names[3]]], - marker = list(size = other_point_size, - color = other_cell_color), - showlegend = FALSE - ) - } - - if (show_NN_network) { - edges <- plotly_network( - annotated_network_DT, - "from_Dim.1", "from_Dim.2", "from_Dim.3", - "to_Dim.1", "to_Dim.2", "to_Dim.3" - ) - if (is.null(nn_network_alpha)) { - nn_network_alpha <- 0.5 - } else if (is.character(nn_network_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - nn_network_alpha <- 0.5 - } - - dpl <- dpl %>% plotly::add_trace( - name = network_name, - mode = "lines", - type = "scatter3d", - data = edges, - x = ~x, y = ~y, z = ~z, - line = list(color = nn_network_color), - opacity = nn_network_alpha - ) - } - if ((show_cluster_center == TRUE | show_center_label == TRUE) & - !is.null(cell_color)) { - annotated_DT_centers <- annotated_DT_selected[, .( - center_1 = stats::median(get(dim_names[1])), - center_2 = stats::median(get(dim_names[2])), - center_3 = stats::median(get(dim_names[3])) - ), - by = cell_color - ] - annotated_DT_centers[[cell_color]] <- as.factor( - annotated_DT_centers[[cell_color]]) - if (show_cluster_center == TRUE) { - dpl <- dpl %>% - plotly::add_trace( - mode = "markers", - type = "scatter3d", - data = annotated_DT_centers, - x = ~center_1, - y = ~center_2, - z = ~center_3, - color = annotated_DT_centers[[cell_color]], - colors = cell_color_code, - marker = list(size = 2, symbol = "x", symbols = "x"), - legendgroup = annotated_DT_centers[[cell_color]], - showlegend = FALSE - ) - } - if (show_center_label == TRUE) { - message(" center label is not clear to see in 3D plot. - You can shut it down with show_center_label = FALSE") - dpl <- dpl %>% - plotly::add_trace( - mode = "text", - type = "scatter3d", - data = annotated_DT_centers, - x = ~center_1, - y = ~center_2, - z = ~center_3, - text = annotated_DT_centers[[cell_color]], - legendgroup = annotated_DT_centers[[cell_color]], - showlegend = FALSE - ) - } - } - if (dim_reduction_to_use == "pca") { - x_name <- paste0("pca", "-", dim_names[1]) - y_name <- paste0("pca", "-", dim_names[2]) - z_name <- paste0("pca", "-", dim_names[3]) - x_title <- sprintf("%s explains %.02f%% of variance", - x_name, var_expl_vec[1]) - y_title <- sprintf("%s explains %.02f%% of variance", - y_name, var_expl_vec[2]) - z_title <- sprintf("%s explains %.02f%% of variance", - z_name, var_expl_vec[3]) - } else { - x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") - y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") - z_title <- paste(dim_reduction_to_use, dim_names[3], sep = " ") - } - } - - - - ############ spatial plot ########## - if (is.null(sdimx) | is.null(sdimy)) { - # cat('first and second dimension need to be defined, default is - # first 2 \n') - sdimx <- "sdimx" - sdimy <- "sdimy" - } - - ## 2D plot ## - if (is.null(sdimz)) { - spl <- plotly::plot_ly() - - if (show_spatial_network == TRUE) { - if (is.null(spatial_network)) { - stop("No usable spatial network specified! Please choose - a network with spatial_network_name=xxx") - } else { - if (is.null(spatial_network_alpha)) { - spatial_network_alpha <- 0.5 - } else if (is.character(spatial_network_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - spatial_network_alpha <- 0.5 - } - spl <- spl %>% plotly::add_segments( - name = spatial_network_name, - type = "scatter", - x = spatial_network[["sdimx_begin"]], - y = spatial_network[["sdimy_begin"]], - xend = spatial_network[["sdimx_end"]], - yend = spatial_network[["sdimy_end"]], - line = list( - color = spatial_network_color, - width = 0.5 - ), - opacity = spatial_network_alpha - ) - } - } - - - if (show_spatial_grid == TRUE) { - if (is.null(spatial_grid)) { - stop("No usable spatial grid specified! Please choose a - network with spatial_grid_name=xxx") - } else { - if (is.null(spatial_grid_color)) { - spatial_grid_color <- "black" - } - edges <- plotly_grid(spatial_grid) - spl <- spl %>% plotly::add_segments( - name = "spatial_grid", - type = "scatter", - data = edges, - x = ~x, - y = ~y, - xend = ~x_end, - yend = ~y_end, - line = list( - color = spatial_grid_color, - width = 1 - ), - opacity = spatial_grid_alpha - ) - } - } - if (is.null(cell_color)) { - # cell_color = "lightblue" - spl <- spl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_selected[[sdimx]], - y = annotated_DT_selected[[sdimy]], - # color = "lightblue", - # colors = "lightblue", - marker = list( - size = spatial_point_size, - color = "lightblue" - ), - showlegend = FALSE - ) - } else if (cell_color %in% colnames(annotated_DT_selected)) { - if (color_as_factor) { - annotated_DT_selected[[cell_color]] <- as.factor( - annotated_DT_selected[[cell_color]] - ) - } - - - spl <- spl %>% - plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_selected[[sdimx]], - y = annotated_DT_selected[[sdimy]], - color = annotated_DT_selected[[cell_color]], - colors = cell_color_code, - legendgroup = annotated_DT_selected[[cell_color]], - marker = list(size = spatial_point_size), - showlegend = FALSE - ) - } else { - stop("cell_color doesn't exist!\n") - } - if (show_other_cells == TRUE) { - spl <- spl %>% plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_other[[sdimx]], - y = annotated_DT_other[[sdimy]], - marker = list(size = other_point_size, - color = other_cell_color), - showlegend = FALSE - ) - } - spl <- spl %>% plotly::layout( - xaxis = list(title = "X"), - yaxis = list(title = "Y"), - legend = list(x = 100, y = 0.5, - font = list(family = "sans-serif", - size = legend_text_size)) - ) - } - - - ## 3D plot ## - else { - axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) - - ratio <- plotly_axis_scale_3D(annotated_DT_selected, - sdimx = sdimx, sdimy = sdimy, sdimz = sdimz, - mode = axis_scale, custom_ratio = custom_ratio - ) - spl <- plotly::plot_ly(scene = "scene2") - if (!is.null(cell_color)) { - if (cell_color %in% colnames(annotated_DT_selected)) { - annotated_DT_selected[[cell_color]] <- as.factor( - annotated_DT_selected[[cell_color]]) - spl <- spl %>% - plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_selected[[sdimx]], - y = annotated_DT_selected[[sdimy]], - z = annotated_DT_selected[[sdimz]], - color = annotated_DT_selected[[cell_color]], - colors = cell_color_code, - legendgroup = annotated_DT_selected[[cell_color]], - marker = list(size = spatial_point_size), - showlegend = FALSE - ) - } else { - stop("cell_color doesn't exist!\n") - } - } else { - spl <- spl %>% - plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_selected$sdimx, - y = annotated_DT_selected$sdimy, - z = annotated_DT_selected$sdimz, - color = "lightblue", - colors = "lightblue", - # legendgroup = annotated_DT_selected[[cell_color]], - marker = list(size = spatial_point_size), - showlegend = FALSE - ) - } - if (show_other_cells == TRUE) { - spl <- spl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_other[[sdimx]], - y = annotated_DT_other[[sdimy]], - z = annotated_DT_other[[sdimz]], - marker = list(size = other_point_size, - color = other_cell_color), - showlegend = FALSE - ) - } - if (show_spatial_network == TRUE) { - if (is.null(spatial_network)) { - stop("No usable spatial network specified! Please choose a - network with spatial_network_name=xxx") - } else { - if (is.null(spatial_network_alpha)) { - spatial_network_alpha <- 0.5 - } else if (is.character(spatial_network_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - spatial_network_alpha <- 0.5 - } - edges <- plotly_network(spatial_network) - - spl <- spl %>% plotly::add_trace( - name = "sptial network", - mode = "lines", - type = "scatter3d", - data = edges, - x = ~x, y = ~y, z = ~z, - line = list(color = spatial_network_color), - opacity = spatial_network_alpha - ) - } - } - - if (show_spatial_grid == TRUE) { - message("3D grid is not clear to view\n") - } - } - - - - - if (is.null(dim3_to_use) & is.null(sdimz)) { - if (plot_alignment == "vertical") { - combo_plot <- plotly::subplot(dpl, spl, nrows = 2, - titleX = TRUE, titleY = TRUE) - } else { - combo_plot <- plotly::subplot(dpl, spl, titleX = TRUE, - titleY = TRUE) - } - } else if (!is.null(dim3_to_use) & is.null(sdimz)) { - if (plot_alignment == "vertical") { - combo_plot <- plotly::subplot(dpl, spl, nrows = 2, titleX = TRUE, - titleY = TRUE) %>% - plotly::layout(scene = list( - domain = list(x = c(0, 1), y = c(0, 0.5)), - xaxis = list(title = x_title), - yaxis = list(title = y_title), - zaxis = list(title = z_title) - )) - } else { - combo_plot <- plotly::subplot(dpl, spl, titleX = TRUE, - titleY = TRUE) %>% - plotly::layout(scene = list( - domain = list(x = c(0, 0.5), y = c(0, 1)), - xaxis = list(title = x_title), - yaxis = list(title = y_title), - zaxis = list(title = z_title) - )) - } - } else if (is.null(dim3_to_use) & !is.null(sdimz)) { - if (plot_alignment == "vertical") { - combo_plot <- plotly::subplot(dpl, spl, nrows = 2, titleX = TRUE, - titleY = TRUE) %>% - plotly::layout(scene2 = list( - domain = list(x = c(0, 1), y = c(0.5, 1)), - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - )) - } else { - combo_plot <- plotly::subplot(dpl, spl, titleX = TRUE, - titleY = TRUE) %>% - plotly::layout(scene2 = list( - domain = list(x = c(0.5, 1), y = c(0, 1)), - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - )) - } - } else if (!is.null(dim3_to_use) & !is.null(sdimz)) { - if (plot_alignment == "vertical") { - combo_plot <- plotly::subplot(dpl, spl, nrows = 2, titleX = TRUE, - titleY = TRUE) %>% - plotly::layout( - scene = list( - domain = list(x = c(0, 1), y = c(0, 0.5)), - xaxis = list(title = x_title), - yaxis = list(title = y_title), - zaxis = list(title = z_title) - ), - scene2 = list( - domain = list(x = c(0, 1), y = c(0.5, 1)), - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ) - ) - } else { - combo_plot <- plotly::subplot(dpl, spl, titleX = TRUE, - titleY = TRUE) %>% - plotly::layout( - scene = list( - domain = list(x = c(0, 0.5), y = c(0, 1)), - xaxis = list(title = x_title), - yaxis = list(title = y_title), - zaxis = list(title = z_title) - ), - scene2 = list( - domain = list(x = c(0.5, 1), y = c(0, 1)), - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ) - ) - } - } - - show_plot <- ifelse(is.null(show_plot), - readGiottoInstructions(gobject, param = "show_plot"), - show_plot) - save_plot <- ifelse(is.null(save_plot), - readGiottoInstructions(gobject, param = "save_plot"), - save_plot) - return_plot <- ifelse(is.null(return_plot), - readGiottoInstructions(gobject, param = "return_plot"), - return_plot) - - ## print plot - if (show_plot == TRUE) { - print(combo_plot) - } - - ## save plot - if (save_plot == TRUE) { - do.call("all_plots_save_function", - c(list(gobject = gobject, plot_object = combo_plot, - default_save_name = default_save_name), save_param)) - } - - ## return plot - if (return_plot == TRUE) { - return(combo_plot) - } -} - - - - -# ** #### -# ** feature 3D plot #### - -#' @title spatFeatPlot3D -#' @name spatFeatPlot3D -#' @description Visualize cells and gene expression according to spatial -#' coordinates -#' @inheritParams data_access_params -#' @inheritParams plot_output_params -#' @param spat_loc_name name of spatial locations to use -#' @param expression_values gene expression values to use -#' @param feats feats to show -#' @param spat_enr_names names of spatial enrichment results to include -#' -#' @param cluster_column cluster column to select groups -#' @param select_cell_groups select subset of cells/clusters based on -#' cell_color parameter -#' @param select_cells select subset of cells based on cell IDs -#' @param show_other_cells display not selected cells -#' @param other_cell_color color of not selected cells -#' @param other_point_size size of not selected cells -#' -#' @param genes_high_color color represents high gene expression -#' @param genes_mid_color color represents middle gene expression -#' @param genes_low_color color represents low gene expression -#' @param show_network show underlying spatial network -#' @param network_color color of spatial network -#' @param spatial_network_name name of spatial network to use -#' @param edge_alpha alpha of edges -#' @param show_grid show spatial grid -#' @param spatial_grid_name name of spatial grid to use -#' -#' @param point_size size of point (cell) -#' @param show_legend show legend -#' -#' @param axis_scale the way to scale the axis -#' @param custom_ratio customize the scale of the plot -#' @param x_ticks set the number of ticks on the x-axis -#' @param y_ticks set the number of ticks on the y-axis -#' @param z_ticks set the number of ticks on the z-axis -#' @param ... additional params to pass -#' @family spatial gene expression visualizations -#' @returns plotly -#' @examples -#' g <- GiottoData::loadGiottoMini("starmap") -#' spatFeatPlot3D(g, feats = "Slc17a7") -#' -#' @export -spatFeatPlot3D <- function(gobject, - spat_unit = NULL, - feat_type = NULL, - spat_loc_name = "raw", - expression_values = c("normalized", "scaled", "custom"), - feats, - spat_enr_names = NULL, - show_network = FALSE, - network_color = NULL, - spatial_network_name = "Delaunay_network", - edge_alpha = NULL, - cluster_column = NULL, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = FALSE, - other_cell_color = "lightgrey", - other_point_size = 1, - genes_high_color = NULL, - genes_mid_color = "white", - genes_low_color = "blue", - show_grid = FALSE, - spatial_grid_name = "spatial_grid", - point_size = 2, - show_legend = TRUE, - axis_scale = c("cube", "real", "custom"), - custom_ratio = NULL, - x_ticks = NULL, - y_ticks = NULL, - z_ticks = NULL, - show_plot = NULL, - return_plot = NULL, - save_plot = NULL, - save_param = list(), - default_save_name = "spatFeatPlot3D", - ... -) { - - # Set feat_type and spat_unit - spat_unit <- set_default_spat_unit( - gobject = gobject, - spat_unit = spat_unit - ) - feat_type <- set_default_feat_type( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type - ) - - # data.table variables - cell_ID <- NULL - - selected_genes <- feats - - values <- match.arg(expression_values, c("normalized", "scaled", "custom")) - expr_values <- getExpression( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - values = values, - output = "matrix" - ) - - # only keep genes that are in the dataset - selected_genes <- selected_genes[selected_genes %in% rownames(expr_values)] - - # get selected feature expression values in data.table format - if (length(selected_genes) == 1) { - subset_expr_data <- expr_values[rownames(expr_values) %in% - selected_genes, ] - t_sub_expr_data_DT <- data.table::data.table( - "selected_gene" = subset_expr_data, - "cell_ID" = colnames(expr_values)) - data.table::setnames(t_sub_expr_data_DT, - "selected_gene", selected_genes) - } else { - subset_expr_data <- expr_values[rownames(expr_values) %in% - selected_genes, ] - t_sub_expr_data <- t_flex(subset_expr_data) - t_sub_expr_data_DT <- data.table::as.data.table( - as.matrix(t_sub_expr_data)) - t_sub_expr_data_DT[, cell_ID := rownames(t_sub_expr_data)] - } - - - ## extract cell locations - cell_locations <- getSpatialLocations( - gobject = gobject, - spat_unit = spat_unit, - name = spat_loc_name, - output = "data.table" - ) - if (is.null(cell_locations)) { - return(NULL) - } - - - ## extract spatial network - if (show_network == TRUE) { - spatial_network <- get_spatialNetwork(gobject, - spat_unit = spat_unit, - name = spatial_network_name, - output = "networkDT" - ) - } else { - spatial_network <- NULL - } - - ## extract spatial grid - if (show_grid == TRUE) { - spatial_grid <- get_spatialGrid(gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spatial_grid_name - ) - } else { - spatial_grid <- NULL - } - - ## extract cell metadata - cell_metadata <- try( - expr = combineMetadata( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spat_loc_name = spat_loc_name, - spat_enr_names = spat_enr_names - ), - silent = TRUE - ) - - - if (inherits(cell_metadata, "try-error")) { - cell_locations_metadata <- cell_locations - } else if (nrow(cell_metadata) == 0) { - cell_locations_metadata <- cell_locations - } else { - cell_locations_metadata <- cell_metadata - } - - - if (!is.null(select_cells) & !is.null(select_cell_groups)) { - message("You have selected both individual cell IDs and a group - of cells") - group_cell_IDs <- cell_locations_metadata[get(cluster_column) %in% - select_cell_groups][["cell_ID"]] - select_cells <- unique(c(select_cells, group_cell_IDs)) - } else if (!is.null(select_cell_groups)) { - select_cells <- cell_locations_metadata[get(cluster_column) %in% - select_cell_groups][["cell_ID"]] - } - - if (!is.null(select_cells)) { - cell_locations_metadata_other <- cell_locations_metadata[ - !cell_locations_metadata$cell_ID %in% select_cells] - cell_locations_metadata_selected <- cell_locations_metadata[ - cell_locations_metadata$cell_ID %in% select_cells] - spatial_network <- spatial_network[spatial_network$to %in% - select_cells & spatial_network$from %in% select_cells] - - # if specific cells are selected - cell_locations_metadata <- cell_locations_metadata_selected - } - - cell_locations_metadata_genes <- merge(cell_locations_metadata, - t_sub_expr_data_DT, by = "cell_ID") - - - - ## plotting ## - axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) - - ratio <- plotly_axis_scale_3D(cell_locations_metadata_genes, - sdimx = "sdimx", sdimy = "sdimy", sdimz = "sdimz", - mode = axis_scale, custom_ratio = custom_ratio - ) - - - ## spatial network data - if (!is.null(spatial_network) & show_network == TRUE) { - edges <- plotly_network(spatial_network) - } - - ## Point layer - if (length(selected_genes) > 4) { - stop("\n The max number of genes showed together is 4.Otherwise - it will be too small to see\n - \n If you have more genes to show, please divide them - into groups\n") - } - savelist <- list() - for (i in seq_len(length(selected_genes))) { - gene <- selected_genes[i] - if (!is.null(genes_high_color)) { - if (length(genes_high_color) != length(selected_genes) & - length(genes_high_color) != 1) { - stop("\n The number of genes and their corresbonding do - not match\n") - } else if (length(genes_high_color) == 1) { - genes_high_color <- rep(genes_high_color, - length(selected_genes)) - } - } else { - genes_high_color <- rep("red", length(selected_genes)) - } - pl <- plotly::plot_ly( - name = gene, - scene = paste("scene", i, sep = "") - ) %>% - plotly::add_trace( - data = cell_locations_metadata_genes, - type = "scatter3d", mode = "markers", - x = ~sdimx, y = ~sdimy, z = ~sdimz, - marker = list(size = point_size), - color = cell_locations_metadata_genes[[gene]], - colors = c(genes_low_color, genes_mid_color, - genes_high_color[i]) - ) - - if (show_other_cells == TRUE) { - pl <- pl %>% plotly::add_trace( - name = "unselected cells", - data = cell_locations_metadata_other, - type = "scatter3d", mode = "markers", - x = ~sdimx, y = ~sdimy, z = ~sdimz, - marker = list(size = other_point_size, color = other_cell_color) - ) - } - - - ## plot spatial network - if (show_network == TRUE) { - if (is.null(network_color)) { - network_color <- "lightblue" - } - if (is.null(edge_alpha)) { - edge_alpha <- 0.5 - } else if (is.character(edge_alpha)) { - edge_alpha <- 0.5 - message("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set") - } - pl <- pl %>% plotly::add_trace( - name = "sptial network", - mode = "lines", - type = "scatter3d", - data = edges, - x = ~x, y = ~y, z = ~z, - line = list(color = network_color, width = 0.5), - opacity = edge_alpha, - showlegend = FALSE - ) - } - - - ## plot spatial grid - if (!is.null(spatial_grid) & show_grid == TRUE) { - message("spatial grid is not clear in 3D plot") - } - - pl <- pl %>% plotly::colorbar(title = gene) - savelist[[gene]] <- pl - } - - - if (length(savelist) == 1) { - cowplot <- savelist[[1]] %>% plotly::layout(scene = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - )) - } else if (length(savelist) == 2) { - cowplot <- plotly::subplot(savelist) %>% - plotly::layout( - scene = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - scene2 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - # annotations = annotations, - legend = list(x = 100, y = 0) - ) - } else if (length(savelist) == 3) { - cowplot <- plotly::subplot(savelist) %>% - plotly::layout( - scene = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - scene2 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - scene3 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - legend = list(x = 100, y = 0) - ) - } else if (length(savelist) == 4) { - cowplot <- plotly::subplot(savelist) %>% - plotly::layout( - scene = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - scene2 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - scene3 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - scene4 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ), - legend = list(x = 100, y = 0) - ) - } - - - show_plot <- ifelse(is.null(show_plot), - readGiottoInstructions(gobject, param = "show_plot"), - show_plot) - save_plot <- ifelse(is.null(save_plot), - readGiottoInstructions(gobject, param = "save_plot"), - save_plot) - return_plot <- ifelse(is.null(return_plot), - readGiottoInstructions(gobject, param = "return_plot"), - return_plot) - ## print plot - if (show_plot == TRUE) { - print(cowplot) - } - - ## save plot - if (save_plot == TRUE) { - do.call("all_plots_save_function", - c(list(gobject = gobject, plot_object = cowplot, - default_save_name = default_save_name), save_param)) - } - - ## return plot - if (return_plot == TRUE) { - return(cowplot) - } -} - -#' @describeIn spatFeatPlot3D deprecated -#' @export -spatGenePlot3D <- function(...) { - deprecate_warn( - when = "0.2.0", - what = "spatGenePlot3D()", - with = "spatFeatPlot3D()" - ) - spatFeatPlot3D(...) -} - - -#' @title dimFeatPlot3D -#' @name dimFeatPlot3D -#' @description Visualize cells and gene expression according to -#' dimension reduction coordinates -#' @inheritParams data_access_params -#' @inheritParams plot_output_params -#' @param expression_values gene expression values to use -#' @param genes genes to show -#' @param dim_reduction_to_use dimension reduction to use -#' @param dim_reduction_name dimension reduction name -#' @param dim1_to_use dimension to use on x-axis -#' @param dim2_to_use dimension to use on y-axis -#' @param dim3_to_use dimension to use on z-axis -#' -#' @param show_NN_network show underlying NN network -#' @param nn_network_to_use type of NN network to use (kNN vs sNN) -#' @param network_name name of NN network to use, if show_NN_network = TRUE -#' @param network_color color of NN network -#' -#' @param cluster_column cluster column to select groups -#' @param select_cell_groups select subset of cells/clusters based on -#' cell_color parameter -#' @param select_cells select subset of cells based on cell IDs -#' @param show_other_cells display not selected cells -#' @param other_cell_color color of not selected cells -#' @param other_point_size size of not selected cells -#' -#' @param edge_alpha column to use for alpha of the edges -#' @param point_size size of point (cell) -#' -#' @param genes_high_color color for high expression levels -#' @param genes_mid_color color for medium expression levels -#' @param genes_low_color color for low expression levels -#' -#' @param show_legend show legend -#' @details Description of parameters. -#' @family dimension reduction gene expression visualizations -#' @returns plotly -#' @examples -#' g <- GiottoData::loadGiottoMini("starmap") -#' -#' dimFeatPlot3D(g, genes = "Slc17a7", dim_reduction_name = "3D_umap") -#' @export -dimFeatPlot3D <- function( - gobject, - feat_type = NULL, - spat_unit = NULL, - expression_values = c("normalized", "scaled", "custom"), - genes = NULL, - dim_reduction_to_use = "umap", - dim_reduction_name = "umap", - dim1_to_use = 1, - dim2_to_use = 2, - dim3_to_use = 3, - show_NN_network = FALSE, - nn_network_to_use = "sNN", - network_name = "sNN.pca", - network_color = "lightgray", - cluster_column = NULL, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = TRUE, - other_cell_color = "lightgrey", - other_point_size = 1, - edge_alpha = NULL, - point_size = 2, - genes_high_color = NULL, - genes_mid_color = "white", - genes_low_color = "blue", - show_legend = TRUE, - show_plot = NULL, - return_plot = NULL, - save_plot = NULL, - save_param = list(), - default_save_name = "dimFeatPlot3D") { - # Set feat_type and spat_unit - spat_unit <- set_default_spat_unit( - gobject = gobject, - spat_unit = spat_unit - ) - feat_type <- set_default_feat_type( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type - ) - - ## select genes ## - selected_genes <- genes - values <- match.arg(expression_values, c("normalized", "scaled", "custom")) - expr_values <- getExpression( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - values = values, - output = "matrix" - ) - - # only keep genes that are in the dataset - selected_genes <- selected_genes[selected_genes %in% rownames(expr_values)] - - # - if (length(selected_genes) == 1) { - subset_expr_data <- expr_values[ - rownames(expr_values) %in% selected_genes, ] - t_sub_expr_data_DT <- data.table::data.table( - "selected_gene" = subset_expr_data, - "cell_ID" = colnames(expr_values)) - data.table::setnames( - t_sub_expr_data_DT, "selected_gene", selected_genes) - } else { - subset_expr_data <- expr_values[ - rownames(expr_values) %in% selected_genes, ] - t_sub_expr_data <- t_flex(subset_expr_data) - t_sub_expr_data_DT <- data.table::as.data.table( - as.matrix(t_sub_expr_data)) - - # data.table variables - cell_ID <- NULL - - t_sub_expr_data_DT[, cell_ID := rownames(t_sub_expr_data)] - } - - - ## dimension reduction ## - dim_dfr <- getDimReduction(gobject, - reduction = "cells", - reduction_method = dim_reduction_to_use, - name = dim_reduction_name, - output = "data.table" - ) - dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use, dim3_to_use)] - dim_names <- colnames(dim_dfr) - dim_DT <- data.table::as.data.table(dim_dfr) - dim_DT[, cell_ID := rownames(dim_dfr)] - - ## annotated cell metadata - cell_metadata <- pDataDT(gobject, - feat_type = feat_type, - spat_unit = spat_unit - ) - annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") - - - - # create input for network - if (show_NN_network == TRUE) { - # nn_network - selected_nn_network <- getNearestNetwork( - gobject = gobject, - feat_type = feat_type, - spat_unit = spat_unit, - nn_type = nn_network_to_use, - name = network_name, - output = "igraph" - ) - network_DT <- data.table::as.data.table(igraph::as_data_frame( - selected_nn_network, what = "edges")) - - # annotated network - old_dim_names <- dim_names - - annotated_network_DT <- merge( - network_DT, dim_DT, by.x = "from", by.y = "cell_ID") - from_dim_names <- paste0("from_", old_dim_names) - data.table::setnames(annotated_network_DT, old = old_dim_names, - new = from_dim_names) - - annotated_network_DT <- merge( - annotated_network_DT, dim_DT, by.x = "to", by.y = "cell_ID") - to_dim_names <- paste0("to_", old_dim_names) - data.table::setnames(annotated_network_DT, old = old_dim_names, - new = to_dim_names) - } - - - ## create subsets if needed - if (!is.null(select_cells) & !is.null(select_cell_groups)) { - if (is.null(cluster_column)) { - stop("\n selection of cells is based on cell_color paramter, - which is a metadata column \n") - } - message("You have selected both individual cell IDs and a group - of cells") - group_cell_IDs <- annotated_DT[get(cluster_column) %in% - select_cell_groups][["cell_ID"]] - select_cells <- unique(c(select_cells, group_cell_IDs)) - } else if (!is.null(select_cell_groups)) { - select_cells <- annotated_DT[get(cluster_column) %in% - select_cell_groups][["cell_ID"]] - } - - if (!is.null(select_cells)) { - annotated_DT_other <- annotated_DT[ - !annotated_DT$cell_ID %in% select_cells] - annotated_DT_selected <- annotated_DT[ - annotated_DT$cell_ID %in% select_cells] - - if (show_NN_network == TRUE) { - annotated_network_DT <- annotated_network_DT[ - annotated_network_DT$to %in% select_cells & - annotated_network_DT$from %in% select_cells] - } - - # if specific cells are selected - annotated_DT <- annotated_DT_selected - } - - ## if no subsets are required - if (is.null(select_cells) & is.null(select_cell_groups)) { - annotated_DT_selected <- annotated_DT - annotated_DT_other <- NULL - } - - ## merge gene info - annotated_gene_DT <- merge(annotated_DT, t_sub_expr_data_DT, by = "cell_ID") - - - - ## visualize multipe plots ## - ## 3D plots ## - - - if (show_NN_network == TRUE) { - edges <- plotly_network( - annotated_network_DT, - "from_Dim.1", "from_Dim.2", "from_Dim.3", - "to_Dim.1", "to_Dim.2", "to_Dim.3" - ) - } - ## Point layer - if (length(selected_genes) > 4) { - stop("\n The max number of genes showed together is 4.Otherwise - it will be too small to see\n - \n If you have more genes to show, please divide them into - groups\n") - } - if (!is.null(genes_high_color)) { - if (length(genes_high_color) != length(selected_genes) & - length(genes_high_color) != 1) { - stop("\n The number of genes and their corresbonding do not - match\n") - } - } else if (is.null(genes_high_color)) { - genes_high_color <- rep("red", length(selected_genes)) - } else { - genes_high_color <- rep(genes_high_color, length(selected_genes)) - } - - titleX <- title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") - titleY <- title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") - titleZ <- title <- paste(dim_reduction_to_use, dim_names[3], sep = " ") - savelist <- list() - for (i in seq_len(length(selected_genes))) { - gene <- selected_genes[i] - - pl <- plotly::plot_ly(name = gene, scene = paste("scene", i, sep = "")) - pl <- pl %>% plotly::add_trace( - data = annotated_gene_DT, type = "scatter3d", mode = "markers", - x = annotated_gene_DT[[dim_names[1]]], - y = annotated_gene_DT[[dim_names[2]]], - z = annotated_gene_DT[[dim_names[3]]], - color = annotated_gene_DT[[gene]], - colors = c(genes_low_color, genes_mid_color, genes_high_color[i]), - marker = list(size = point_size) - ) - if (show_other_cells == TRUE) { - pl <- pl %>% plotly::add_trace( - name = "unselected cells", - data = annotated_DT_other, - type = "scatter3d", mode = "markers", - x = annotated_DT_other[[dim_names[1]]], - y = annotated_DT_other[[dim_names[2]]], - z = annotated_DT_other[[dim_names[3]]], - marker = list(size = other_point_size, color = other_cell_color) - ) - } - - ## plot spatial network - if (show_NN_network == TRUE) { - pl <- pl %>% plotly::add_trace( - name = "sptial network", mode = "lines", - type = "scatter3d", opacity = edge_alpha, - showlegend = FALSE, - data = edges, - x = ~x, y = ~y, z = ~z, - line = list( - color = network_color, - width = 0.5 - ) - ) - } - pl <- pl %>% plotly::colorbar(title = gene) - savelist[[gene]] <- pl - } - - if (length(savelist) == 1) { - cowplot <- savelist[[1]] %>% plotly::layout(scene = list( - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - )) - } else if (length(savelist) == 2) { - cowplot <- plotly::subplot( - savelist, titleX = TRUE, titleY = TRUE) %>% - plotly::layout( - scene = list( - domain = list(x = c(0, 0.5), y = c(0, 1)), - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - ), - scene2 = list( - domain = list(x = c(0.5, 1), y = c(0, 1)), - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - ), - legend = list(x = 100, y = 0) - ) - } else if (length(savelist) == 3) { - cowplot <- plotly::subplot( - savelist, titleX = TRUE, titleY = TRUE) %>% - plotly::layout( - scene = list( - domain = list(x = c(0, 0.5), y = c(0, 0.5)), - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - ), - scene2 = list( - domain = list(x = c(0.5, 1), y = c(0, 0.5)), - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - ), - scene3 = list( - domain = list(x = c(0, 0.5), y = c(0.5, 1)), - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - ), - legend = list(x = 100, y = 0) - ) - } else if (length(savelist) == 4) { - cowplot <- plotly::subplot(savelist) %>% - plotly::layout( - scene = list( - domain = list(x = c(0, 0.5), y = c(0, 0.5)), - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - ), - scene2 = list( - domain = list(x = c(0.5, 1), y = c(0, 0.5)), - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - ), - scene3 = list( - domain = list(x = c(0, 0.5), y = c(0.5, 1)), - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - ), - scene4 = list( - domain = list(x = c(0.5, 1), y = c(0.5, 1)), - xaxis = list(title = titleX), - yaxis = list(title = titleY), - zaxis = list(title = titleZ) - ), - legend = list(x = 100, y = 0) - ) - } - - show_plot <- ifelse(is.null(show_plot), - readGiottoInstructions(gobject, param = "show_plot"), - show_plot) - save_plot <- ifelse(is.null(save_plot), - readGiottoInstructions(gobject, param = "save_plot"), - save_plot) - return_plot <- ifelse(is.null(return_plot), - readGiottoInstructions(gobject, param = "return_plot"), - return_plot) - ## print plot - if (show_plot == TRUE) { - print(cowplot) - } - - ## save plot - if (save_plot == TRUE) { - do.call("all_plots_save_function", - c(list(gobject = gobject, plot_object = cowplot, - default_save_name = default_save_name), save_param)) - } - - ## return plot - if (return_plot == TRUE) { - return(cowplot) - } -} - -#' @describeIn dimFeatPlot3D deprecated -#' @param ... additional params to pass -#' @export -dimGenePlot3D <- function(...) { - deprecate_warn( - when = "0.2.0", - what = "dimGenePlot3D()", - with = "dimFeatPlot3D()" - ) - dimFeatPlot3D(...) -} - - - -#' @title spatDimFeatPlot3D -#' @name spatDimFeatPlot3D -#' @description Visualize cells according to spatial AND dimension -#' reduction coordinates in ggplot mode -#' @inheritParams data_access_params -#' @inheritParams plot_output_params -#' @param spat_loc_name name of spatial locations to use -#' @param expression_values gene expression values to use -#' @param plot_alignment direction to align plot -#' @param dim_reduction_to_use dimension reduction to use -#' @param dim_reduction_name dimension reduction name -#' @param dim1_to_use dimension to use on x-axis -#' @param dim2_to_use dimension to use on y-axis -#' @param dim3_to_use dimension to use on z-axis -#' @param sdimx spatial dimension to use on x-axis -#' @param sdimy spatial dimension to use on y-axis -#' @param sdimz spatial dimension to use on z-axis -#' @param genes genes to show -#' -#' @param cluster_column cluster column to select groups -#' @param select_cell_groups select subset of cells/clusters based on -#' cell_color parameter -#' @param select_cells select subset of cells based on cell IDs -#' @param show_other_cells display not selected cells -#' @param other_cell_color color of not selected cells -#' @param other_point_size size of not selected cells -#' -#' @param dim_point_size dim reduction plot: point size -#' @param show_NN_network show underlying NN network -#' @param nn_network_to_use type of NN network to use (kNN vs sNN) -#' @param nn_network_color color of NN network -#' @param nn_network_alpha alpha of NN network -#' @param network_name name of NN network to use, if show_NN_network = TRUE -#' -#' @param label_size size of labels -#' @param genes_high_color color for high expression levels -#' @param genes_mid_color color for medium expression levels -#' @param genes_low_color color for low expression levels -#' -#' @param show_spatial_network show spatial network (boolean) -#' @param spatial_network_name name of spatial network to use -#' @param spatial_network_color color of spatial network -#' @param spatial_network_alpha alpha of spatial network -#' -#' @param show_spatial_grid show spatial grid (boolean) -#' @param spatial_grid_name name of spatial grid to use -#' @param spatial_grid_color color of spatial grid -#' @param spatial_grid_alpha alpha of spatial grid -#' -#' @param spatial_point_size spatial plot: point size -#' @param legend_text_size size of legend -#' -#' @param axis_scale the way to scale the axis -#' @param custom_ratio customize the scale of the plot -#' @param x_ticks set the number of ticks on the x-axis -#' @param y_ticks set the number of ticks on the y-axis -#' @param z_ticks set the number of ticks on the z-axis -#' @details Description of parameters. -#' @family spatial and dimension reduction gene expression visualizations -#' @returns plotly -#' @examples -#' g <- GiottoData::loadGiottoMini("starmap") -#' spatDimFeatPlot3D(g, genes = "Slc17a7") -#' -#' @export -spatDimFeatPlot3D <- function(gobject, - feat_type = NULL, - spat_unit = NULL, - spat_loc_name = NULL, - expression_values = c("normalized", "scaled", "custom"), - plot_alignment = c("horizontal", "vertical"), - dim_reduction_to_use = "umap", - dim_reduction_name = "umap", - dim1_to_use = 1, - dim2_to_use = 2, - dim3_to_use = NULL, - sdimx = "sdimx", - sdimy = "sdimy", - sdimz = "sdimz", - genes, - cluster_column = NULL, - select_cell_groups = NULL, - select_cells = NULL, - show_other_cells = TRUE, - other_cell_color = "lightgrey", - other_point_size = 1.5, - show_NN_network = FALSE, - nn_network_to_use = "sNN", - nn_network_color = "lightgrey", - nn_network_alpha = 0.5, - network_name = "sNN.pca", - label_size = 16, - genes_low_color = "blue", - genes_mid_color = "white", - genes_high_color = "red", - dim_point_size = 3, - show_spatial_network = FALSE, - spatial_network_name = "Delaunay_network", - spatial_network_color = "lightgray", - spatial_network_alpha = 0.5, - show_spatial_grid = FALSE, - spatial_grid_name = "spatial_grid", - spatial_grid_color = NULL, - spatial_grid_alpha = 0.5, - spatial_point_size = 3, - legend_text_size = 12, - axis_scale = c("cube", "real", "custom"), - custom_ratio = NULL, - x_ticks = NULL, - y_ticks = NULL, - z_ticks = NULL, - show_plot = NULL, - return_plot = NULL, - save_plot = NULL, - save_param = list(), - default_save_name = "spatDimFeatPlot3D") { - # Set feat_type and spat_unit - spat_unit <- set_default_spat_unit( - gobject = gobject, - spat_unit = spat_unit - ) - feat_type <- set_default_feat_type( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type - ) - - # data.table variables - cell_ID <- NULL - - plot_alignment <- match.arg(plot_alignment, - choices = c("horizontal", "vertical")) - - ########### data prepare ########### - ## select genes ## - if (length(genes) > 1) { - warning("\n Now 3D mode can just accept one gene, only the first - gene will be plot\n") - genes <- genes[1] - } - selected_genes <- genes - values <- match.arg(expression_values, c("normalized", "scaled", "custom")) - expr_values <- get_expression_values( - gobject = gobject, - spat_unit = spat_unit, - feat_type = feat_type, - values = values, - output = "matrix" - ) - - # only keep genes that are in the dataset - selected_genes <- selected_genes[selected_genes %in% rownames(expr_values)] - subset_expr_data <- expr_values[rownames(expr_values) %in% selected_genes, ] - t_sub_expr_data_DT <- data.table::data.table( - "selected_gene" = subset_expr_data, "cell_ID" = colnames(expr_values)) - data.table::setnames(t_sub_expr_data_DT, "selected_gene", selected_genes) - - - ## dimension reduction ## - dim_dfr <- get_dimReduction(gobject, - reduction = "cells", - reduction_method = dim_reduction_to_use, - name = dim_reduction_name, - output = "data.table" - ) - dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use, dim3_to_use)] - dim_names <- colnames(dim_dfr) - dim_DT <- data.table::as.data.table(dim_dfr) - dim_DT[, cell_ID := rownames(dim_dfr)] - - - ## annotated cell metadata - cell_metadata <- pDataDT(gobject, - feat_type = feat_type, - spat_unit = spat_unit - ) - cell_locations <- get_spatial_locations( - gobject = gobject, - spat_unit = spat_unit, - spat_loc_name = spat_loc_name, - output = "data.table" - ) - if (is.null(cell_locations)) { - return(NULL) - } - - annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") - annotated_DT <- merge(annotated_DT, cell_locations, by = "cell_ID") - annotated_DT <- merge(annotated_DT, t_sub_expr_data_DT, by = "cell_ID") - - - ## nn network - if (show_NN_network) { - # nn_network - selected_nn_network <- get_NearestNetwork( - gobject = gobject, - feat_type = feat_type, - spat_unit = spat_unit, - nn_network_to_use = nn_network_to_use, - network_name = network_name, - output = "igraph" - ) - network_DT <- data.table::as.data.table(igraph::as_data_frame( - selected_nn_network, what = "edges")) - - # annotated network - old_dim_names <- dim_names - - annotated_network_DT <- merge( - network_DT, dim_DT, by.x = "from", by.y = "cell_ID") - from_dim_names <- paste0("from_", old_dim_names) - data.table::setnames( - annotated_network_DT, old = old_dim_names, new = from_dim_names) - - annotated_network_DT <- merge(annotated_network_DT, dim_DT, - by.x = "to", by.y = "cell_ID") - to_dim_names <- paste0("to_", old_dim_names) - data.table::setnames( - annotated_network_DT, old = old_dim_names, new = to_dim_names) - } - - - ## extract spatial network - if (show_spatial_network == TRUE) { - spatial_network <- get_spatialNetwork(gobject, - spat_unit = spat_unit, - name = spatial_network_name, - output = "networkDT" - ) - } else { - spatial_network <- NULL - } - - ## extract spatial grid - if (show_spatial_grid == TRUE) { - spatial_grid <- get_spatialGrid(gobject, - spat_unit = spat_unit, - feat_type = feat_type, - spatial_grid_name - ) - } else { - spatial_grid <- NULL - } - - - ## select subset of cells ## - if (!is.null(select_cells) & !is.null(select_cell_groups)) { - if (is.null(cluster_column)) { - stop("\n selection of cells is based on cell_color paramter, - which is a metadata column \n") - } - message("You have selected both individual cell IDs and a group - of cells") - group_cell_IDs <- annotated_DT[get(cluster_column) %in% - select_cell_groups][["cell_ID"]] - select_cells <- unique(c(select_cells, group_cell_IDs)) - } else if (!is.null(select_cell_groups)) { - select_cells <- annotated_DT[get(cluster_column) %in% - select_cell_groups][["cell_ID"]] - } - - if (!is.null(select_cells)) { - annotated_DT_other <- annotated_DT[ - !annotated_DT$cell_ID %in% select_cells] - annotated_DT_selected <- annotated_DT[ - annotated_DT$cell_ID %in% select_cells] - - if (show_NN_network == TRUE) { - annotated_network_DT <- annotated_network_DT[ - annotated_network_DT$to %in% select_cells & - annotated_network_DT$from %in% select_cells] - } - if (show_spatial_network == TRUE) { - spatial_network <- spatial_network[ - spatial_network$to %in% select_cells & - spatial_network$from %in% select_cells] - } - - # if specific cells are selected - annotated_DT <- annotated_DT_selected - } - - ## if no subsets are required - if (is.null(select_cells) & is.null(select_cell_groups)) { - annotated_DT_selected <- annotated_DT - annotated_DT_other <- NULL - } - - - - - ########### dim plot ########### - # 2D plot - if (is.null(dim3_to_use)) { - dpl <- plotly::plot_ly() - if (show_NN_network == TRUE) { - if (is.null(nn_network_alpha)) { - nn_network_alpha <- 0.5 - } else if (is.character(nn_network_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - nn_network_alpha <- 0.5 - } - dpl <- dpl %>% plotly::add_segments( - name = network_name, - type = "scatter", - x = annotated_network_DT[[from_dim_names[1]]], - y = annotated_network_DT[[from_dim_names[2]]], - xend = annotated_network_DT[[to_dim_names[1]]], - yend = annotated_network_DT[[to_dim_names[2]]], - line = list( - color = nn_network_color, - width = 0.5 - ), - opacity = nn_network_alpha - ) - } - - dpl <- dpl %>% - plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT[[dim_names[1]]], - y = annotated_DT[[dim_names[2]]], - color = annotated_DT[[selected_genes]], - colors = c( - genes_low_color, genes_mid_color, - genes_high_color - ), - marker = list(size = dim_point_size), - showlegend = FALSE - ) - - if (show_other_cells == TRUE) { - dpl <- dpl %>% - plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_other[[dim_names[1]]], - y = annotated_DT_other[[dim_names[2]]], - marker = list( - size = other_point_size, - color = other_cell_color - ), - showlegend = FALSE - ) - } - - x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") - y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") - - dpl <- dpl %>% plotly::layout( - xaxis = list(title = x_title), - yaxis = list(title = y_title), - legend = list(x = 100, y = 0.5, - font = list(family = "sans-serif", - size = legend_text_size)) - ) - } - # 3D plot - else if (!is.null(dim3_to_use)) { - dpl <- plotly::plot_ly(scene = "scene1") - - dpl <- dpl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT[[dim_names[1]]], - y = annotated_DT[[dim_names[2]]], - z = annotated_DT[[dim_names[3]]], - color = annotated_DT[[selected_genes]], - colors = c(genes_low_color, genes_mid_color, genes_high_color), - marker = list(size = dim_point_size), - showlegend = FALSE - ) - # legendgroup = annotated_DT[[cell_color]]) - if (show_other_cells == TRUE) { - dpl <- dpl %>% plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_other[[dim_names[1]]], - y = annotated_DT_other[[dim_names[2]]], - z = annotated_DT_other[[dim_names[3]]], - marker = list(size = other_point_size, - color = other_cell_color), - showlegend = FALSE - ) - } - - if (show_NN_network) { - edges <- plotly_network( - annotated_network_DT, - "from_Dim.1", "from_Dim.2", "from_Dim.3", - "to_Dim.1", "to_Dim.2", "to_Dim.3" - ) - if (is.null(nn_network_alpha)) { - nn_network_alpha <- 0.5 - } else if (is.character(nn_network_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - nn_network_alpha <- 0.5 - } - - dpl <- dpl %>% plotly::add_trace( - name = network_name, - mode = "lines", - type = "scatter3d", - data = edges, - x = ~x, y = ~y, z = ~z, - line = list(color = nn_network_color), - opacity = nn_network_alpha - ) - } - - - x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") - y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") - z_title <- paste(dim_reduction_to_use, dim_names[3], sep = " ") - } - dpl <- dpl %>% plotly::colorbar(title = selected_genes) - - - ########### spatial plot ########### - if (is.null(sdimx) | is.null(sdimy)) { - # cat('first and second dimenion need to be defined, - # default is first 2 \n') - sdimx <- "sdimx" - sdimy <- "sdimy" - } - - # 2D plot - if (is.null(sdimz)) { - spl <- plotly::plot_ly() - - if (show_spatial_network == TRUE) { - if (is.null(spatial_network)) { - stop("No usable spatial network specified! Please choose a - network with spatial_network_name=xxx") - } else { - if (is.null(spatial_network_alpha)) { - spatial_network_alpha <- 0.5 - } else if (is.character(spatial_network_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - spatial_network_alpha <- 0.5 - } - spl <- spl %>% plotly::add_segments( - name = spatial_network_name, - type = "scatter", - x = spatial_network[["sdimx_begin"]], - y = spatial_network[["sdimy_begin"]], - xend = spatial_network[["sdimx_end"]], - yend = spatial_network[["sdimy_end"]], - line = list( - color = spatial_network_color, - width = 0.5 - ), - opacity = spatial_network_alpha - ) - } - } - if (show_spatial_grid == TRUE) { - if (is.null(spatial_grid)) { - stop("No usable spatial grid specified! Please choose a - network with spatial_grid_name=xxx") - } else { - if (is.null(spatial_grid_color)) { - spatial_grid_color <- "black" - } - edges <- plotly_grid(spatial_grid) - spl <- spl %>% plotly::add_segments( - name = "spatial_grid", - type = "scatter", - data = edges, - x = ~x, - y = ~y, - xend = ~x_end, - yend = ~y_end, - line = list( - color = spatial_grid_color, - width = 1 - ), - opacity = spatial_grid_alpha - ) - } - } - - spl <- spl %>% - plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT[[sdimx]], - y = annotated_DT[[sdimy]], - color = annotated_DT[[selected_genes]], - colors = c( - genes_low_color, genes_mid_color, - genes_high_color - ), - marker = list(size = spatial_point_size), - showlegend = FALSE - ) - if (show_other_cells == TRUE) { - spl <- spl %>% - plotly::add_trace( - type = "scatter", mode = "markers", - x = annotated_DT_other[[sdimx]], - y = annotated_DT_other[[sdimy]], - marker = list( - size = other_point_size, - color = other_cell_color - ), - showlegend = FALSE - ) - } - - spl <- spl %>% plotly::layout( - xaxis = list(title = "X"), - yaxis = list(title = "Y"), - legend = list(x = 100, y = 0.5, - font = list(family = "sans-serif", - size = legend_text_size)) - ) - } - - - # 3D plot - else { - axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) - ratio <- plotly_axis_scale_3D(annotated_DT, - sdimx = sdimx, sdimy = sdimy, sdimz = sdimz, - mode = axis_scale, custom_ratio = custom_ratio - ) - - - spl <- plotly::plot_ly(scene = "scene2") - - spl <- spl %>% - plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT[[sdimx]], - y = annotated_DT[[sdimy]], - z = annotated_DT[[sdimz]], - color = annotated_DT[[selected_genes]], - colors = c( - genes_low_color, genes_mid_color, - genes_high_color - ), - # legendgroup = annotated_DT[[cell_color]], - marker = list(size = spatial_point_size), - showlegend = FALSE - ) - if (show_other_cells == TRUE) { - spl <- spl %>% - plotly::add_trace( - type = "scatter3d", mode = "markers", - x = annotated_DT_other[[sdimx]], - y = annotated_DT_other[[sdimy]], - z = annotated_DT_other[[sdimz]], - marker = list( - size = other_point_size, - color = other_cell_color - ), - showlegend = FALSE - ) - } - - if (show_spatial_network == TRUE) { - if (is.null(spatial_network)) { - stop("No usable spatial network specified! Please choose a - network with spatial_network_name=xxx") - } else { - if (is.null(spatial_network_alpha)) { - spatial_network_alpha <- 0.5 - } else if (is.character(spatial_network_alpha)) { - warning("Edge_alpha for plotly mode is not adjustable yet. - Default 0.5 will be set\n") - spatial_network_alpha <- 0.5 - } - edges <- plotly_network(spatial_network) - - spl <- spl %>% plotly::add_trace( - name = "sptial network", - mode = "lines", - type = "scatter3d", - data = edges, - x = ~x, y = ~y, z = ~z, - line = list(color = spatial_network_color), - opacity = spatial_network_alpha - ) - } - } - - if (show_spatial_grid == TRUE) { - message("3D grid is not clear to view") - } - } - - - - spl <- plotly::hide_colorbar(spl) - if (is.null(dim3_to_use) & is.null(sdimz)) { - if (plot_alignment == "vertical") { - combo_plot <- plotly::subplot( - dpl, spl, nrows = 2, titleX = TRUE, titleY = TRUE) - } else { - combo_plot <- plotly::subplot( - dpl, spl, titleX = TRUE, titleY = TRUE) - } - } else if (!is.null(dim3_to_use) & is.null(sdimz)) { - if (plot_alignment == "vertical") { - combo_plot <- plotly::subplot( - dpl, spl, nrows = 2, titleX = TRUE, titleY = TRUE) %>% - plotly::layout(scene = list( - domain = list(x = c(0, 1), y = c(0, 0.5)), - xaxis = list(title = x_title), - yaxis = list(title = y_title), - zaxis = list(title = z_title) - )) - } else { - combo_plot <- plotly::subplot( - dpl, spl, titleX = TRUE, titleY = TRUE) %>% - plotly::layout(scene = list( - domain = list(x = c(0, 0.5), y = c(0, 1)), - xaxis = list(title = x_title), - yaxis = list(title = y_title), - zaxis = list(title = z_title) - )) - } - } else if (is.null(dim3_to_use) & !is.null(sdimz)) { - if (plot_alignment == "vertical") { - combo_plot <- plotly::subplot( - dpl, spl, nrows = 2, titleX = TRUE, titleY = TRUE) %>% - plotly::layout(scene2 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - )) - } else { - combo_plot <- plotly::subplot( - dpl, spl, titleX = TRUE, titleY = TRUE) %>% - plotly::layout(scene2 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - )) - } - } else if (!is.null(dim3_to_use) & !is.null(sdimz)) { - if (plot_alignment == "vertical") { - combo_plot <- plotly::subplot( - dpl, spl, nrows = 2, titleX = TRUE, titleY = TRUE) %>% - plotly::layout( - scene = list( - domain = list(x = c(0, 1), y = c(0, 0.5)), - xaxis = list(title = x_title), - yaxis = list(title = y_title), - zaxis = list(title = z_title) - ), - scene2 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ) - ) - } else { - combo_plot <- plotly::subplot( - dpl, spl, titleX = TRUE, titleY = TRUE) %>% - plotly::layout( - scene = list( - domain = list(x = c(0, 0.5), y = c(0, 1)), - xaxis = list(title = x_title), - yaxis = list(title = y_title), - zaxis = list(title = z_title) - ), - scene2 = list( - xaxis = list(title = "X", nticks = x_ticks), - yaxis = list(title = "Y", nticks = y_ticks), - zaxis = list(title = "Z", nticks = z_ticks), - aspectmode = "manual", - aspectratio = list( - x = ratio[[1]], - y = ratio[[2]], - z = ratio[[3]] - ) - ) - ) - } - } - - show_plot <- ifelse(is.null(show_plot), - readGiottoInstructions(gobject, param = "show_plot"), - show_plot) - save_plot <- ifelse(is.null(save_plot), - readGiottoInstructions(gobject, param = "save_plot"), - save_plot) - return_plot <- ifelse(is.null(return_plot), - readGiottoInstructions(gobject, param = "return_plot"), - return_plot) - - ## print plot - if (show_plot == TRUE) { - print(combo_plot) - } - - ## save plot - if (save_plot == TRUE) { - do.call("all_plots_save_function", - c(list(gobject = gobject, plot_object = combo_plot, - default_save_name = default_save_name), save_param)) - } - - ## return plot - if (return_plot == TRUE) { - return(combo_plot) - } -} - -#' @describeIn spatDimFeatPlot3D deprecated -#' @param ... additional params to pass -#' @export -spatDimGenePlot3D <- function(...) { - deprecate_warn( - when = "0.2.0", - what = "spatDimGenePlot3D()", - with = "spatDimFeatPlot3D()" - ) - spatDimFeatPlot3D(...) -} - - - diff --git a/R/vis_spatial_plotly.R b/R/vis_spatial_plotly.R new file mode 100644 index 0000000..8902e82 --- /dev/null +++ b/R/vis_spatial_plotly.R @@ -0,0 +1,4144 @@ + +# * #### +## 3-D plotly #### +## ----------- ## + +# ** dimension plot #### + + +#' @title .dimPlot_2d_plotly +#' @name .dimPlot_2d_plotly +#' @description Visualize cells at their 2D dimension reduction coordinates +#' with plotly +#' @returns plotly object +#' @keywords internal +.dimPlot_2d_plotly <- function(gobject, + spat_unit = NULL, + feat_type = NULL, + dim_reduction_to_use = "umap", + dim_reduction_name = "umap", + dim1_to_use = 1, + dim2_to_use = 2, + spat_enr_names = NULL, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = TRUE, + other_cell_color = "lightgrey", + other_point_size = 0.5, + show_NN_network = FALSE, + nn_network_to_use = "sNN", + network_name = "sNN.pca", + color_as_factor = TRUE, + cell_color = NULL, + cell_color_code = NULL, + show_cluster_center = FALSE, + show_center_label = TRUE, + center_point_size = 4, + label_size = 4, + edge_alpha = NULL, + point_size = 5) { + # Set feat_type and spat_unit + spat_unit <- set_default_spat_unit( + gobject = gobject, + spat_unit = spat_unit + ) + feat_type <- set_default_feat_type( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type + ) + + # data.table variables + cell_ID <- NULL + + ## dimension reduction ## + dim_dfr <- get_dimReduction( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + reduction = "cells", + reduction_method = dim_reduction_to_use, + name = dim_reduction_name, + output = "data.table" + ) + + dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use)] + dim_names <- colnames(dim_dfr) + dim_DT <- data.table::as.data.table(dim_dfr) + dim_DT[, "cell_ID" := rownames(dim_dfr)] + + + ## annotated cell metadata + cell_metadata <- combineMetadata( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spat_enr_names = spat_enr_names + ) + annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") + + + # create input for network + if (show_NN_network == TRUE) { + # nn_network + selected_nn_network <- get_NearestNetwork( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + nn_network_to_use = nn_network_to_use, + network_name = network_name, + output = "igraph" + ) + network_DT <- data.table::as.data.table(igraph::as_data_frame( + selected_nn_network, what = "edges")) + + # annotated network + old_dim_names <- dim_names + + annotated_network_DT <- merge(network_DT, dim_DT, by.x = "from", + by.y = "cell_ID") + from_dim_names <- paste0("from_", old_dim_names) + data.table::setnames(annotated_network_DT, old = old_dim_names, + new = from_dim_names) + + annotated_network_DT <- merge(annotated_network_DT, dim_DT, + by.x = "to", by.y = "cell_ID") + to_dim_names <- paste0("to_", old_dim_names) + data.table::setnames(annotated_network_DT, old = old_dim_names, + new = to_dim_names) + } + + + if (dim_reduction_to_use == "pca") { + pca_object <- get_dimReduction( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + reduction = "cells", + reduction_method = dim_reduction_to_use, + name = dim_reduction_name, + output = "dimObj" + ) + eigenvalues <- slot(pca_object, "misc")$eigenvalues + + if (!is.null(eigenvalues)) { + total <- sum(eigenvalues) + var_expl_vec <- (eigenvalues / total) * 100 + dim1_x_variance <- var_expl_vec[dim1_to_use] + dim2_y_variance <- var_expl_vec[dim2_to_use] + } + } + + + if (!is.null(select_cells) & !is.null(select_cell_groups)) { + if (is.null(cell_color)) { + stop("\n selection of cells is based on cell_color paramter, + which is a metadata column \n") + } + message("You have selected both individual cell IDs and a group + of cells") + group_cell_IDs <- annotated_DT[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + select_cells <- unique(c(select_cells, group_cell_IDs)) + } else if (!is.null(select_cell_groups)) { + select_cells <- annotated_DT[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + } + + + if (!is.null(select_cells)) { + annotated_DT_other <- annotated_DT[!annotated_DT$cell_ID %in% + select_cells] + annotated_DT_selected <- annotated_DT[annotated_DT$cell_ID %in% + select_cells] + + if (show_NN_network == TRUE) { + annotated_network_DT <- annotated_network_DT[ + annotated_network_DT$to %in% select_cells & + annotated_network_DT$from %in% select_cells] + } + + # if specific cells are selected + # annotated_DT = annotated_DT_selected + } + + + ## if no subsets are required + if (is.null(select_cells) & is.null(select_cell_groups)) { + annotated_DT_selected <- annotated_DT + annotated_DT_other <- NULL + } + + + ## annotated_DT_selected = all selected cells or all cells if no selection + ## annotated_DT_other = all not selected cells or NULL if no selection + + + pl <- plotly::plot_ly() + if (show_NN_network == TRUE) { + if (is.null(edge_alpha)) { + edge_alpha <- 0.5 + } else if (is.character(edge_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + edge_alpha <- 0.5 + } + + pl <- pl %>% plotly::add_segments( + name = network_name, + type = "scatter", + x = annotated_network_DT[[from_dim_names[1]]], + y = annotated_network_DT[[from_dim_names[2]]], + xend = annotated_network_DT[[to_dim_names[1]]], + yend = annotated_network_DT[[to_dim_names[2]]], + line = list( + color = "lightgray", + width = 0.5 + ), + opacity = edge_alpha + ) + } + + if (is.null(cell_color)) { + cell_color <- "lightblue" + pl <- pl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_selected[[dim_names[1]]], + y = annotated_DT_selected[[dim_names[2]]], + color = cell_color, + colors = cell_color, + marker = list(size = point_size) + ) + } else if (cell_color %in% colnames(annotated_DT_selected)) { + if (is.null(cell_color_code)) { + number_colors <- length(unique(annotated_DT[[cell_color]])) + cell_color_code <- set_default_color_discrete_cell( + instrs = instructions(gobject))(n = number_colors) + } + if (color_as_factor) { + annotated_DT_selected[[cell_color]] <- as.factor( + annotated_DT_selected[[cell_color]]) + } + + + pl <- pl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_selected[[dim_names[1]]], + y = annotated_DT_selected[[dim_names[2]]], + color = annotated_DT_selected[[cell_color]], + colors = cell_color_code, + legendgroup = annotated_DT_selected[[cell_color]], + marker = list(size = point_size) + ) + + if (!is.null(select_cells) & show_other_cells) { + pl <- pl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_other[[dim_names[1]]], + y = annotated_DT_other[[dim_names[2]]], + # legendgroup = annotated_DT[[cell_color]], + marker = list(size = other_point_size, + color = other_cell_color), + showlegend = FALSE + ) + } + + if (show_cluster_center == TRUE | show_center_label == TRUE) { + annotated_DT_centers <- annotated_DT_selected[, .( + center_1 = stats::median(get(dim_names[1])), + center_2 = stats::median(get(dim_names[2])) + ), + by = cell_color + ] + annotated_DT_centers[[cell_color]] <- as.factor( + annotated_DT_centers[[cell_color]]) + if (show_cluster_center == TRUE) { + pl <- pl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_centers[["center_1"]], + y = annotated_DT_centers[["center_2"]], + color = annotated_DT_centers[[cell_color]], + colors = cell_color_code, + legendgroup = annotated_DT_centers[[cell_color]], + marker = list(size = center_point_size, symbol = "x", + symbols = "x"), + showlegend = FALSE + ) + } + + if (show_center_label == TRUE) { + pl <- pl %>% + plotly::add_text( + x = annotated_DT_centers[["center_1"]], + y = annotated_DT_centers[["center_2"]], + type = "scatter", mode = "text", + text = annotated_DT_centers[[cell_color]], + textposition = "middle right", + textfont = list(color = "#000000", size = 16), + showlegend = FALSE + ) + } + } + } else { + stop("cell_color does not exist!\n") + } + + + + if (dim_reduction_to_use == "pca") { + if (!is.null(eigenvalues)) { + x_name <- paste0("pca", "-", dim_names[1]) + y_name <- paste0("pca", "-", dim_names[2]) + x_title <- sprintf("%s explains %.02f%% of variance", + x_name, var_expl_vec[1]) + y_title <- sprintf("%s explains %.02f%% of variance", y_name, + var_expl_vec[2]) + } + } else { + x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") + y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") + } + pl <- pl %>% plotly::layout( + xaxis = list(title = x_title), + yaxis = list(title = y_title), + legend = list(x = 100, y = 0.5, font = list(family = "sans-serif", + size = 12)) + ) + + return(pl) +} + + +#' @title .dimPlot_3d_plotly +#' @name .dimPlot_3d_plotly +#' @description Visualize cells at their 3D dimension reduction coordinates +#' with plotly +#' @returns plotly object +#' @keywords internal +.dimPlot_3d_plotly <- function(gobject, + spat_unit = NULL, + feat_type = NULL, + dim_reduction_to_use = "umap", + dim_reduction_name = "umap", + dim1_to_use = 1, + dim2_to_use = 2, + dim3_to_use = 3, + spat_enr_names = NULL, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = TRUE, + other_cell_color = "lightgrey", + other_point_size = 0.5, + show_NN_network = FALSE, + nn_network_to_use = "sNN", + network_name = "sNN.pca", + color_as_factor = TRUE, + cell_color = NULL, + cell_color_code = NULL, + show_cluster_center = FALSE, + show_center_label = TRUE, + center_point_size = 4, + label_size = 4, + edge_alpha = NULL, + point_size = 1) { + # Set feat_type and spat_unit + spat_unit <- set_default_spat_unit( + gobject = gobject, + spat_unit = spat_unit + ) + feat_type <- set_default_feat_type( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type + ) + + # data.table variables + cell_ID <- NULL + + ## dimension reduction ## + dim_dfr <- get_dimReduction( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + reduction = "cells", + reduction_method = dim_reduction_to_use, + name = dim_reduction_name, + output = "data.table" + ) + dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use, dim3_to_use)] + dim_names <- colnames(dim_dfr) + dim_DT <- data.table::as.data.table(dim_dfr) + dim_DT[, cell_ID := rownames(dim_dfr)] + + + ## annotated cell metadata + cell_metadata <- combineMetadata( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spat_enr_names = spat_enr_names + ) + annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") + + + # create input for network + if (show_NN_network == TRUE) { + # nn_network + selected_nn_network <- get_NearestNetwork( + gobject = gobject, spat_unit = spat_unit, + feat_type = feat_type, + nn_network_to_use = nn_network_to_use, + network_name = network_name, + output = "igraph" + ) + network_DT <- data.table::as.data.table(igraph::as_data_frame( + selected_nn_network, what = "edges")) + + # annotated network + old_dim_names <- dim_names + + annotated_network_DT <- merge(network_DT, dim_DT, by.x = "from", + by.y = "cell_ID") + from_dim_names <- paste0("from_", old_dim_names) + data.table::setnames(annotated_network_DT, old = old_dim_names, + new = from_dim_names) + + annotated_network_DT <- merge(annotated_network_DT, dim_DT, + by.x = "to", by.y = "cell_ID") + to_dim_names <- paste0("to_", old_dim_names) + data.table::setnames(annotated_network_DT, old = old_dim_names, + new = to_dim_names) + } + + if (dim_reduction_to_use == "pca") { + pca_object <- get_dimReduction( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + reduction = "cells", + reduction_method = dim_reduction_to_use, + name = dim_reduction_name, + output = "dimObj" + ) + + eigenvalues <- slot(pca_object, "misc")$eigenvalues + if (!is.null(eigenvalues)) { + total <- sum(eigenvalues) + var_expl_vec <- (eigenvalues / total) * 100 + dim1_x_variance <- var_expl_vec[dim1_to_use] + dim2_y_variance <- var_expl_vec[dim2_to_use] + } + } + + ## create subsets if needed + if (!is.null(select_cells) & !is.null(select_cell_groups)) { + if (is.null(cell_color)) { + stop("\n selection of cells is based on cell_color parameter, + which is a metadata column \n") + } + message("You have selected both individual cell IDs and a group of + cells") + group_cell_IDs <- annotated_DT[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + select_cells <- unique(c(select_cells, group_cell_IDs)) + } else if (!is.null(select_cell_groups)) { + select_cells <- annotated_DT[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + } + + if (!is.null(select_cells)) { + annotated_DT_other <- annotated_DT[!annotated_DT$cell_ID %in% + select_cells] + annotated_DT_selected <- annotated_DT[annotated_DT$cell_ID %in% + select_cells] + + if (show_NN_network == TRUE) { + annotated_network_DT <- annotated_network_DT[ + annotated_network_DT$to %in% select_cells & + annotated_network_DT$from %in% select_cells] + } + + # if specific cells are selected + annotated_DT <- annotated_DT_selected + } + + ## if no subsets are required + if (is.null(select_cells) & is.null(select_cell_groups)) { + annotated_DT_selected <- annotated_DT + annotated_DT_other <- NULL + } + + ## annotated_DT_selected = all selected cells or all cells if no selection + ## annotated_DT_other = all not selected cells or NULL if no selection + + + pl <- plotly::plot_ly() + if (is.null(cell_color)) { + cell_color <- "lightblue" + pl <- pl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_selected[[dim_names[1]]], + y = annotated_DT_selected[[dim_names[2]]], + z = annotated_DT_selected[[dim_names[3]]], + color = cell_color, + colors = cell_color, + marker = list(size = 2), + legendgroup = annotated_DT_selected[[cell_color]] + ) + } else { + if (cell_color %in% colnames(annotated_DT_selected)) { + if (is.null(cell_color_code)) { + number_colors <- length( + unique(annotated_DT_selected[[cell_color]])) + cell_color_code <- set_default_color_discrete_cell( + instrs = instructions(gobject))(n = number_colors) + } + if (color_as_factor) { + annotated_DT_selected[[cell_color]] <- as.factor( + annotated_DT_selected[[cell_color]]) + } + + pl <- pl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_selected[[dim_names[1]]], + y = annotated_DT_selected[[dim_names[2]]], + z = annotated_DT_selected[[dim_names[3]]], + color = annotated_DT_selected[[cell_color]], + colors = cell_color_code, + marker = list(size = point_size), + legendgroup = annotated_DT_selected[[cell_color]] + ) + + if (!is.null(select_cells) & show_other_cells) { + pl <- pl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_other[[dim_names[1]]], + y = annotated_DT_other[[dim_names[2]]], + z = annotated_DT_other[[dim_names[3]]], + # colors = other_cell_color, + marker = list(size = other_point_size, + color = other_cell_color), + showlegend = FALSE + ) + } + + + if (show_cluster_center == TRUE | show_center_label == TRUE) { + annotated_DT_centers <- annotated_DT_selected[, .( + center_1 = stats::median(get(dim_names[1])), + center_2 = stats::median(get(dim_names[2])), + center_3 = stats::median(get(dim_names[3])) + ), + by = cell_color + ] + annotated_DT_centers[[cell_color]] <- as.factor( + annotated_DT_centers[[cell_color]]) + if (show_cluster_center == TRUE) { + pl <- pl %>% plotly::add_trace( + mode = "markers", + type = "scatter3d", + data = annotated_DT_centers, + x = ~center_1, + y = ~center_2, + z = ~center_3, + color = annotated_DT_centers[[cell_color]], + colors = cell_color_code, + inherit = FALSE, + marker = list(size = 2, symbol = "x", symbols = "x"), + legendgroup = annotated_DT_centers[[cell_color]], + showlegend = FALSE + ) + } + if (show_center_label == TRUE) { + message(" center label is not clear to see in 3D plot\n You + can shut it down with show_center_label = FALSE") + pl <- pl %>% plotly::add_trace( + mode = "text", + type = "scatter3d", + data = annotated_DT_centers, + x = ~center_1, + y = ~center_2, + z = ~center_3, + text = annotated_DT_centers[[cell_color]], + legendgroup = annotated_DT_centers[[cell_color]], + inherit = FALSE, + showlegend = FALSE + ) + } + } + } else { + stop("cell_color does not exist!\n") + } + } + + if (show_NN_network) { + edges <- plotly_network( + annotated_network_DT, + "from_Dim.1", "from_Dim.2", "from_Dim.3", + "to_Dim.1", "to_Dim.2", "to_Dim.3" + ) + if (is.null(edge_alpha)) { + edge_alpha <- 0.5 + } else if (is.character(edge_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + edge_alpha <- 0.5 + } + + pl <- pl %>% plotly::add_trace( + name = network_name, + mode = "lines", + type = "scatter3d", + data = edges, + x = ~x, y = ~y, z = ~z, + inherit = FALSE, + line = list(color = "lightgray", width = 0.5), + opacity = edge_alpha + ) + } + + if (dim_reduction_to_use == "pca") { + if (!is.null(eigenvalues)) { + x_name <- paste0("pca", "-", dim_names[1]) + y_name <- paste0("pca", "-", dim_names[2]) + z_name <- paste0("pca", "-", dim_names[3]) + x_title <- sprintf("%s explains %.02f%% of variance", + x_name, var_expl_vec[1]) + y_title <- sprintf("%s explains %.02f%% of variance", + y_name, var_expl_vec[2]) + z_title <- sprintf("%s explains %.02f%% of variance", + z_name, var_expl_vec[3]) + } + } else { + x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") + y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") + z_title <- paste(dim_reduction_to_use, dim_names[3], sep = " ") + } + pl <- pl %>% plotly::layout( + scene = list( + xaxis = list(title = x_title), + yaxis = list(title = y_title), + zaxis = list(title = z_title) + ), + legend = list(x = 100, y = 0.5, + font = list(family = "sans-serif", size = 12)) + ) + return(pl) +} + + + + + + + +#' @rdname dimPlot +#' @returns plotly (dimplot3D only) +#' @export +dimPlot3D <- function(gobject, + spat_unit = NULL, + feat_type = NULL, + dim_reduction_to_use = "umap", + dim_reduction_name = "umap", + dim1_to_use = 1, + dim2_to_use = 2, + dim3_to_use = 3, + spat_enr_names = NULL, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = TRUE, + other_cell_color = "lightgrey", + other_point_size = 2, + show_NN_network = FALSE, + nn_network_to_use = "sNN", + network_name = "sNN.pca", + color_as_factor = TRUE, + cell_color = NULL, + cell_color_code = NULL, + show_cluster_center = FALSE, + show_center_label = TRUE, + center_point_size = 4, + label_size = 4, + edge_alpha = NULL, + point_size = 3, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, + save_param = list(), + default_save_name = "dim3D") { + if (is.null(dim3_to_use)) { + message("create 2D plot") + + pl <- .dimPlot_2d_plotly( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + dim_reduction_to_use = dim_reduction_to_use, + dim_reduction_name = dim_reduction_name, + dim1_to_use = dim1_to_use, + dim2_to_use = dim2_to_use, + spat_enr_names = spat_enr_names, + select_cell_groups = select_cell_groups, + select_cells = select_cells, + show_other_cells = show_other_cells, + other_cell_color = other_cell_color, + other_point_size = other_point_size, + show_NN_network = show_NN_network, + nn_network_to_use = nn_network_to_use, + network_name = network_name, + color_as_factor = color_as_factor, + cell_color = cell_color, + cell_color_code = cell_color_code, + show_cluster_center = show_cluster_center, + show_center_label = show_center_label, + center_point_size = center_point_size, + label_size = label_size, + edge_alpha = edge_alpha, + point_size = point_size + ) + } else { + message("create 3D plot") + pl <- .dimPlot_3d_plotly( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + dim_reduction_to_use = dim_reduction_to_use, + dim_reduction_name = dim_reduction_name, + dim1_to_use = dim1_to_use, + dim2_to_use = dim2_to_use, + dim3_to_use = dim3_to_use, + spat_enr_names = spat_enr_names, + select_cell_groups = select_cell_groups, + select_cells = select_cells, + show_other_cells = show_other_cells, + other_cell_color = other_cell_color, + other_point_size = other_point_size, + show_NN_network = show_NN_network, + nn_network_to_use = nn_network_to_use, + network_name = network_name, + color_as_factor = color_as_factor, + cell_color = cell_color, + cell_color_code = cell_color_code, + show_cluster_center = show_cluster_center, + show_center_label = show_center_label, + center_point_size = center_point_size, + label_size = label_size, + edge_alpha = edge_alpha, + point_size = point_size + ) + } + + + show_plot <- ifelse(is.null(show_plot), + readGiottoInstructions(gobject, param = "show_plot"), + show_plot) + save_plot <- ifelse(is.null(save_plot), + readGiottoInstructions(gobject, param = "save_plot"), + save_plot) + return_plot <- ifelse(is.null(return_plot), + readGiottoInstructions(gobject, param = "return_plot"), + return_plot) + + ## print plot + if (show_plot == TRUE) { + print(pl) + } + + ## save plot + if (save_plot == TRUE) { + do.call("all_plots_save_function", + c(list(gobject = gobject, plot_object = pl, + default_save_name = default_save_name), save_param)) + } + + ## return plot + if (return_plot == TRUE) { + return(pl) + } +} + + +#' @title plotUMAP_3D +#' @name plotUMAP_3D +#' @description Visualize cells according to dimension reduction coordinates +#' @param gobject giotto object +#' @param dim_reduction_name name of UMAP +#' @param default_save_name default save name of UMAP plot +#' @inheritDotParams dimPlot3D -gobject -dim_reduction_to_use +#' -dim_reduction_name -default_save_name +#' @details Description of parameters. +#' @family reduced dimension visualizations +#' @returns plotly +#' @examples +#' g <- GiottoData::loadGiottoMini("starmap") +#' plotUMAP_3D(g, dim_reduction_name = "3D_umap") +#' +#' @export +plotUMAP_3D <- function(gobject, + dim_reduction_name = "umap", + default_save_name = "UMAP_3D", + ...) { + dimPlot3D( + gobject = gobject, + dim_reduction_to_use = "umap", + dim_reduction_name = dim_reduction_name, + default_save_name = default_save_name, + ... + ) +} + + +#' @title plotTSNE_3D +#' @name plotTSNE_3D +#' @description Visualize cells according to dimension reduction coordinates +#' @param gobject giotto object +#' @param dim_reduction_name name of TSNE +#' @param default_save_name default save name of TSNE plot +#' @inheritDotParams dimPlot3D -gobject -dim_reduction_to_use +#' -dim_reduction_name -default_save_name +#' @details Description of parameters. +#' @family reduced dimension visualizations +#' @returns plotly +#' @examples +#' g <- GiottoData::loadGiottoMini("starmap") +#' plotTSNE_3D(g) +#' +#' @export +plotTSNE_3D <- function(gobject, + dim_reduction_name = "tsne", + default_save_name = "TSNE_3D", + ...) { + dimPlot3D( + gobject = gobject, + dim_reduction_to_use = "tsne", + dim_reduction_name = dim_reduction_name, + default_save_name = default_save_name, + ... + ) +} + + +#' @title plotPCA_3D +#' @name plotPCA_3D +#' @description Visualize cells according to 3D PCA dimension reduction +#' @param gobject giotto object +#' @param dim_reduction_name name of PCA +#' @param default_save_name default save name of PCA plot +#' @inheritDotParams dimPlot3D -gobject -dim_reduction_to_use +#' -dim_reduction_name -default_save_name +#' @details Description of parameters. +#' @family reduced dimension visualizations +#' @returns plotly +#' @examples +#' g <- GiottoData::loadGiottoMini("starmap") +#' plotPCA_3D(g) +#' +#' @export +plotPCA_3D <- function(gobject, + dim_reduction_name = "pca", + default_save_name = "PCA_3D", + ...) { + dimPlot3D( + gobject = gobject, + dim_reduction_to_use = "pca", + dim_reduction_name = dim_reduction_name, + default_save_name = default_save_name, + ... + ) +} + + + + + + +# ** #### +# ** spatial 3D plot #### + +#' @title .spatPlot_2d_plotly +#' @name .spatPlot_2d_plotly +#' @description Visualize cells at their 2D spatial locations with plotly +#' @returns plotly object +#' @keywords internal +.spatPlot_2d_plotly <- function(gobject, + spat_unit = NULL, + feat_type = NULL, + spat_loc_name = "raw", + sdimx = NULL, + sdimy = NULL, + spat_enr_names = NULL, + point_size = 3, + cell_color = NULL, + cell_color_code = NULL, + color_as_factor = TRUE, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = TRUE, + other_cell_color = "lightgrey", + other_point_size = 0.5, + show_network = FALSE, + spatial_network_name = "spatial_network", + network_color = "lightgray", + network_alpha = 1, + other_cell_alpha = 0.5, + show_grid = FALSE, + spatial_grid_name = "spatial_grid", + grid_color = NULL, + grid_alpha = 1, + show_legend = TRUE, + axis_scale = c("cube", "real", "custom"), + custom_ratio = NULL, + x_ticks = NULL, + y_ticks = NULL, + show_plot = FALSE) { + # Set feat_type and spat_unit + spat_unit <- set_default_spat_unit( + gobject = gobject, + spat_unit = spat_unit + ) + feat_type <- set_default_feat_type( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type + ) + + ## get spatial cell locations + cell_locations <- get_spatial_locations(gobject, + spat_unit = spat_unit, + spat_loc_name = spat_loc_name, + output = "data.table" + ) + if (is.null(cell_locations)) { + return(NULL) + } + + + ## extract spatial network + if (show_network == TRUE) { + spatial_network <- get_spatialNetwork(gobject, + spat_unit = spat_unit, + name = spatial_network_name, + output = "networkDT" + ) + } else { + spatial_network <- NULL + } + + ## extract spatial grid + if (show_grid == TRUE) { + spatial_grid <- get_spatialGrid(gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spatial_grid_name + ) + } else { + spatial_grid <- NULL + } + + ## get cell metadata + cell_metadata <- try( + expr = combineMetadata( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spat_loc_name = spat_loc_name, + spat_enr_names = spat_enr_names + ), + silent = TRUE + ) + + + if (inherits(cell_metadata, "try-error")) { + cell_locations_metadata <- cell_locations + } else if (nrow(cell_metadata) == 0) { + cell_locations_metadata <- cell_locations + } else { + cell_locations_metadata <- cell_metadata + } + + ## create subsets if needed + if (!is.null(select_cells) & !is.null(select_cell_groups)) { + message("You have selected both individual cell IDs and a group + of cells") + group_cell_IDs <- cell_locations_metadata[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + select_cells <- unique(c(select_cells, group_cell_IDs)) + } else if (!is.null(select_cell_groups)) { + select_cells <- cell_locations_metadata[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + } + + + if (!is.null(select_cells)) { + cell_locations_metadata_other <- cell_locations_metadata[ + !cell_locations_metadata$cell_ID %in% select_cells] + cell_locations_metadata_selected <- cell_locations_metadata[ + cell_locations_metadata$cell_ID %in% select_cells] + spatial_network <- spatial_network[spatial_network$to %in% + select_cells & spatial_network$from %in% + select_cells] + + # if specific cells are selected + # cell_locations_metadata = cell_locations_metadata_selected + } else if (is.null(select_cells)) { + cell_locations_metadata_selected <- cell_locations_metadata + cell_locations_metadata_other <- NULL + } + + + + ### set scale + axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) + + ### set ratio + ratio <- plotly_axis_scale_2D(cell_locations, + sdimx = sdimx, + sdimy = sdimy, + mode = axis_scale, + custom_ratio = custom_ratio + ) + + + + pl <- plotly::plot_ly() + + ## create network + if (show_network == TRUE) { + if (is.null(spatial_network)) { + stop("No usable spatial network specified! Please choose a + network with spatial_network_name=xxx") + } else { + if (is.null(network_alpha)) { + network_alpha <- 0.5 + } else if (is.character(network_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + network_alpha <- 0.5 + } + pl <- pl %>% plotly::add_segments( + name = spatial_network_name, + type = "scatter", + x = spatial_network[["sdimx_begin"]], + y = spatial_network[["sdimy_begin"]], + xend = spatial_network[["sdimx_end"]], + yend = spatial_network[["sdimy_end"]], + line = list( + color = network_color, + width = 0.5 + ), + opacity = network_alpha + ) + } + } + + ## create grid + if (show_grid == TRUE) { + if (is.null(spatial_grid)) { + stop("No usable spatial grid specified! Please choose a + network with spatial_grid_name=xxx") + } else { + if (is.null(grid_color)) { + grid_color <- "black" + } + edges <- plotly_grid(spatial_grid) + pl <- pl %>% plotly::add_segments( + name = "spatial_grid", + type = "scatter", + data = edges, + x = ~x, + y = ~y, + xend = ~x_end, + yend = ~y_end, + line = list( + color = grid_color, + width = 1 + ), + opacity = grid_alpha + ) + } + } + + + + if (!is.null(cell_color)) { + if (cell_color %in% colnames(cell_locations_metadata_selected)) { + if (is.null(cell_color_code)) { + number_colors <- length(unique( + cell_locations_metadata_selected[[cell_color]])) + cell_color_code <- set_default_color_discrete_cell( + instrs = instructions(gobject))(n = number_colors) + } + cell_locations_metadata_selected[[cell_color]] <- as.factor( + cell_locations_metadata_selected[[cell_color]]) + pl <- pl %>% plotly::add_trace( + type = "scatter", + mode = "markers", + x = cell_locations_metadata_selected[[sdimx]], + y = cell_locations_metadata_selected[[sdimy]], + color = cell_locations_metadata_selected[[cell_color]], + colors = cell_color_code, + marker = list(size = point_size) + ) + + + if (!is.null(select_cells) & show_other_cells) { + pl <- pl %>% plotly::add_trace( + type = "scatter", + mode = "markers", + data = cell_locations_metadata_other, + name = "unselected cells", + x = ~sdimx, + y = ~sdimy, + marker = list(size = other_point_size, + color = other_cell_color), + opacity = other_cell_alpha + ) + } + } else { + message("cell_color does not exist!") + } + } else { + pl <- pl %>% plotly::add_trace( + type = "scatter", + mode = "markers", + name = "selected cells", + x = cell_locations_metadata_selected[[sdimx]], + y = cell_locations_metadata_selected[[sdimy]], + colors = "lightblue", + marker = list(size = point_size) + ) + + if (!is.null(select_cells) & show_other_cells) { + pl <- pl %>% plotly::add_trace( + type = "scatter", + mode = "markers", + data = cell_locations_metadata_other, + name = "unselected cells", + x = ~sdimx, + y = ~sdimy, + marker = list( + size = other_point_size, + color = other_cell_color + ), + opacity = other_cell_alpha + ) + } + } + + + pl <- pl %>% + plotly::layout( + list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks) + ), + legend = list( + x = 100, y = 0.5, + font = list( + family = "sans-serif", + size = 12 + ) + ) + ) + + + return((pl)) +} + + + +#' @title .spatPlot_3d_plotly +#' @name .spatPlot_3d_plotly +#' @description Visualize cells at their 3D spatial locations with plotly +#' @returns plotly object +#' @keywords internal +.spatPlot_3d_plotly <- function(gobject, + spat_unit = NULL, + feat_type = NULL, + spat_loc_name = "raw", + sdimx = NULL, + sdimy = NULL, + sdimz = NULL, + spat_enr_names = NULL, + point_size = 3, + cell_color = NULL, + cell_color_code = NULL, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = TRUE, + other_cell_color = "lightgrey", + other_point_size = 0.5, + show_network = FALSE, + spatial_network_name = "spatial_network", + network_color = NULL, + network_alpha = 1, + other_cell_alpha = 0.5, + show_grid = FALSE, + spatial_grid_name = "spatial_grid", + title = "", + show_legend = TRUE, + axis_scale = c("cube", "real", "custom"), + custom_ratio = NULL, + x_ticks = NULL, + y_ticks = NULL, + z_ticks = NULL, + show_plot = FALSE) { + # Set feat_type and spat_unit + spat_unit <- set_default_spat_unit( + gobject = gobject, + spat_unit = spat_unit + ) + feat_type <- set_default_feat_type( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type + ) + + ## get spatial cell locations + cell_locations <- get_spatial_locations(gobject, + spat_unit = spat_unit, + spat_loc_name = spat_loc_name, + output = "data.table" + ) + if (is.null(cell_locations)) { + return(NULL) + } + + ## extract spatial network + if (show_network == TRUE) { + spatial_network <- get_spatialNetwork(gobject, + spat_unit = spat_unit, + name = spatial_network_name, + output = "networkDT" + ) + } else { + spatial_network <- NULL + } + + ## extract spatial grid + if (show_grid == TRUE) { + spatial_grid <- get_spatialGrid(gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spatial_grid_name + ) + } else { + spatial_grid <- NULL + } + + ## get cell metadata + cell_metadata <- try( + expr = combineMetadata( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spat_loc_name = spat_loc_name, + spat_enr_names = spat_enr_names + ), + silent = TRUE + ) + + + if (inherits(cell_metadata, "try-error")) { + cell_locations_metadata <- cell_locations + } else if (nrow(cell_metadata) == 0) { + cell_locations_metadata <- cell_locations + } else { + cell_locations_metadata <- cell_metadata + } + + + ## create subsets if needed + if (!is.null(select_cells) & !is.null(select_cell_groups)) { + message("You have selected both individual cell IDs and a group of + cells") + group_cell_IDs <- cell_locations_metadata[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + select_cells <- unique(c(select_cells, group_cell_IDs)) + } else if (!is.null(select_cell_groups)) { + select_cells <- cell_locations_metadata[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + } + + if (!is.null(select_cells)) { + cell_locations_metadata_other <- cell_locations_metadata[ + !cell_locations_metadata$cell_ID %in% select_cells] + cell_locations_metadata_selected <- cell_locations_metadata[ + cell_locations_metadata$cell_ID %in% select_cells] + spatial_network <- spatial_network[spatial_network$to %in% + select_cells & spatial_network$from %in% select_cells] + + # if specific cells are selected + # cell_locations_metadata = cell_locations_metadata_selected + } else if (is.null(select_cells)) { + cell_locations_metadata_selected <- cell_locations_metadata + cell_locations_metadata_other <- NULL + } + + + + ### set scale + axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) + + ### set ratio + ratio <- plotly_axis_scale_3D(cell_locations, + sdimx = sdimx, + sdimy = sdimy, + sdimz = sdimz, + mode = axis_scale, + custom_ratio = custom_ratio + ) + + + + pl <- plotly::plot_ly() + if (!is.null(cell_color)) { + if (cell_color %in% colnames(cell_locations_metadata_selected)) { + if (is.null(cell_color_code)) { + number_colors <- length(unique( + cell_locations_metadata_selected[[cell_color]])) + cell_color_code <- set_default_color_discrete_cell( + instrs = instructions(gobject))(n = number_colors) + } + cell_locations_metadata_selected[[cell_color]] <- as.factor( + cell_locations_metadata_selected[[cell_color]]) + pl <- pl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + data = cell_locations_metadata_selected, + x = ~sdimx, y = ~sdimy, z = ~sdimz, + color = cell_locations_metadata_selected[[cell_color]], + colors = cell_color_code, + marker = list(size = point_size) + ) + + + if (!is.null(select_cells) & show_other_cells) { + pl <- pl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + data = cell_locations_metadata_other, + name = "unselected cells", + x = ~sdimx, + y = ~sdimy, + z = ~sdimz, + marker = list( + size = other_point_size, + color = other_cell_color + ), + opacity = other_cell_alpha + ) + } + } else { + message("cell_color does not exist!") + } + } else { + pl <- pl %>% plotly::add_trace( + type = "scatter3d", + data = cell_locations_metadata_selected, + x = ~sdimx, + y = ~sdimy, + z = ~sdimz, + mode = "markers", + marker = list(size = point_size), + colors = "lightblue", name = "selected cells" + ) + + if (!is.null(select_cells) & show_other_cells) { + pl <- pl %>% plotly::add_trace( + type = "scatter3d", + mode = "markers", + data = cell_locations_metadata_other, + name = "unselected cells", + x = ~sdimx, y = ~sdimy, z = ~sdimz, + marker = list( + size = other_point_size, + color = other_cell_color + ), + opacity = other_cell_alpha + ) + } + } + + + ## plot spatial network + if (!is.null(spatial_network) & show_network == TRUE) { + if (is.null(network_color)) { + network_color <- "red" + } + edges <- plotly_network(spatial_network) + + pl <- pl %>% plotly::add_trace( + name = "sptial network", + mode = "lines", + type = "scatter3d", + data = edges, + x = ~x, + y = ~y, + z = ~z, + line = list(color = network_color, width = 0.5), + opacity = network_alpha + ) + } + + ## plot spatial grid + # 3D grid is not clear to view + + + pl <- pl %>% + plotly::layout( + scene = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + legend = list( + x = 100, y = 0.5, + font = list(family = "sans-serif", size = 12) + ) + ) + + + return(pl) +} + + + + + +#' @rdname spatPlot +#' @param sdimz z-axis dimension name (default = 'sdimy') +#' @param grid_alpha opacity of spatial grid +#' @param axis_scale the way to scale the axis +#' @param custom_ratio customize the scale of the plot +#' @param x_ticks set the number of ticks on the x-axis +#' @param y_ticks set the number of ticks on the y-axis +#' @param z_ticks set the number of ticks on the z-axis +#' @export +spatPlot3D <- function(gobject, + spat_unit = NULL, + feat_type = NULL, + sdimx = "sdimx", + sdimy = "sdimy", + sdimz = "sdimz", + spat_enr_names = NULL, + point_size = 3, + cell_color = NULL, + cell_color_code = NULL, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = TRUE, + other_cell_color = "lightgrey", + other_point_size = 0.5, + other_cell_alpha = 0.5, + show_network = FALSE, + spatial_network_name = "Delaunay_network", + network_color = NULL, + network_alpha = 1, + show_grid = FALSE, + spatial_grid_name = "spatial_grid", + grid_color = NULL, + grid_alpha = 1, + title = "", + show_legend = TRUE, + axis_scale = c("cube", "real", "custom"), + custom_ratio = NULL, + x_ticks = NULL, + y_ticks = NULL, + z_ticks = NULL, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, + save_param = list(), + default_save_name = "spat3D") { + if (is.null(sdimz)) { + message("create 2D plot") + + pl <- .spatPlot_2d_plotly( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + sdimx = sdimx, + sdimy = sdimy, + point_size = point_size, + cell_color = cell_color, + cell_color_code = cell_color_code, + select_cell_groups = select_cell_groups, + select_cells = select_cells, + show_other_cells = show_other_cells, + other_cell_color = other_cell_color, + other_point_size = other_point_size, + show_network = show_network, + network_color = network_color, + network_alpha = network_alpha, + other_cell_alpha = other_cell_alpha, + spatial_network_name = spatial_network_name, + show_grid = show_grid, + grid_color = grid_color, + grid_alpha = grid_alpha, + spatial_grid_name = spatial_grid_name, + show_legend = show_legend, + axis_scale = axis_scale, + custom_ratio = custom_ratio, + x_ticks = x_ticks, + y_ticks = y_ticks, + show_plot = FALSE + ) + } else { + message("create 3D plot") + pl <- .spatPlot_3d_plotly( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + sdimx = sdimx, + sdimy = sdimy, + sdimz = sdimz, + point_size = point_size, + cell_color = cell_color, + cell_color_code = cell_color_code, + select_cell_groups = select_cell_groups, + select_cells = select_cells, + show_other_cells = show_other_cells, + other_cell_color = other_cell_color, + other_point_size = other_point_size, + show_network = show_network, + network_color = network_color, + network_alpha = network_alpha, + other_cell_alpha = other_cell_alpha, + spatial_network_name = spatial_network_name, + spatial_grid_name = spatial_grid_name, + show_legend = show_legend, + axis_scale = axis_scale, + custom_ratio = custom_ratio, + x_ticks = x_ticks, + y_ticks = y_ticks, + z_ticks = z_ticks, + show_plot = FALSE + ) + } + + show_plot <- ifelse(is.null(show_plot), + readGiottoInstructions(gobject, param = "show_plot"), + show_plot) + save_plot <- ifelse(is.null(save_plot), + readGiottoInstructions(gobject, param = "save_plot"), + save_plot) + return_plot <- ifelse(is.null(return_plot), + readGiottoInstructions(gobject, param = "return_plot"), + return_plot) + + ## print plot + if (show_plot == TRUE) { + print(pl) + } + + ## save plot + if (save_plot == TRUE) { + do.call("all_plots_save_function", + c(list(gobject = gobject, plot_object = pl, + default_save_name = default_save_name), save_param)) + } + + ## return plot + if (return_plot == TRUE) { + return(pl) + } +} + + + + + + + + + +# ** #### +# ** spatial & dimension 3D plot #### + +#' @title spatDimPlot3D +#' @name spatDimPlot3D +#' @description Visualize cells according to spatial AND dimension +#' reduction coordinates in plotly mode +#' @inheritParams data_access_params +#' @inheritParams plot_output_params +#' @inheritParams plot_cell_params +#' @param plot_alignment direction to align plot +#' @param dim_reduction_to_use dimension reduction to use +#' @param dim_reduction_name dimension reduction name +#' @param dim1_to_use dimension to use on x-axis +#' @param dim2_to_use dimension to use on y-axis +#' @param dim3_to_use dimension to use on z-axis +#' +#' @param spat_loc_name name for spatial locations +#' @param sdimx = spatial dimension to use on x-axis +#' @param sdimy = spatial dimension to use on y-axis +#' @param sdimz = spatial dimension to use on z-axis +#' +#' @param spat_enr_names names of spatial enrichment results to include +#' @param show_NN_network show underlying NN network +#' @param nn_network_to_use type of NN network to use (kNN vs sNN) +#' @param network_name name of NN network to use, if show_NN_network = TRUE +#' @param show_cluster_center show the center of each cluster +#' @param show_center_label provide a label for each cluster +#' @param center_point_size size of the center point +#' @param label_size size of the center label +#' +#' @param select_cell_groups select subset of cells/clusters based on +#' cell_color parameter +#' @param select_cells select subset of cells based on cell IDs +#' @param show_other_cells display not selected cells +#' @param other_cell_color color of not selected cells +#' @param other_point_size size of not selected cells +#' +#' @param dim_point_size size of points in dim. reduction space +#' @param nn_network_color color of nn network +#' @param nn_network_alpha column to use for alpha of the edges +#' @param show_spatial_network show spatial network +#' @param spatial_network_name name of spatial network to use +#' @param spatial_network_color color of spatial network +#' +#' @param show_spatial_grid show spatial grid +#' @param spatial_grid_name name of spatial grid to use +#' @param spatial_grid_color color of spatial grid +#' @param spatial_grid_alpha alpha of spatial grid +#' @param spatial_point_size size of spatial points +#' @param spatial_network_color color of spatial network +#' @param spatial_network_alpha alpha of spatial network +#' +#' @param axis_scale the way to scale the axis +#' @param custom_ratio customize the scale of the plot +#' @param x_ticks set the number of ticks on the x-axis +#' @param y_ticks set the number of ticks on the y-axis +#' @param z_ticks set the number of ticks on the z-axis +#' @param legend_text_size size of legend +#' @returns plotly +#' @details Description of parameters. +#' @family spatial and dimension reduction visualizations +#' @export +spatDimPlot3D <- function(gobject, + spat_unit = NULL, + feat_type = NULL, + plot_alignment = c("horizontal", "vertical"), + dim_reduction_to_use = "umap", + dim_reduction_name = "umap", + dim1_to_use = 1, + dim2_to_use = 2, + dim3_to_use = 3, + spat_loc_name = NULL, + sdimx = "sdimx", + sdimy = "sdimy", + sdimz = "sdimz", + spat_enr_names = NULL, + show_NN_network = FALSE, + nn_network_to_use = "sNN", + network_name = "sNN.pca", + nn_network_color = "lightgray", + nn_network_alpha = 0.5, + show_cluster_center = FALSE, + show_center_label = TRUE, + center_point_size = 4, + label_size = 16, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = TRUE, + other_cell_color = "lightgrey", + other_point_size = 1.5, + cell_color = NULL, + color_as_factor = TRUE, + cell_color_code = NULL, + dim_point_size = 3, + show_spatial_network = FALSE, + spatial_network_name = "Delaunay_network", + spatial_network_color = "lightgray", + spatial_network_alpha = 0.5, + show_spatial_grid = FALSE, + spatial_grid_name = "spatial_grid", + spatial_grid_color = NULL, + spatial_grid_alpha = 0.5, + spatial_point_size = 3, + axis_scale = c("cube", "real", "custom"), + custom_ratio = NULL, + x_ticks = NULL, + y_ticks = NULL, + z_ticks = NULL, + legend_text_size = 12, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, + save_param = list(), + default_save_name = "spatDimPlot3D") { + # Set feat_type and spat_unit + spat_unit <- set_default_spat_unit( + gobject = gobject, + spat_unit = spat_unit + ) + feat_type <- set_default_feat_type( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type + ) + + # data.table variables + cell_ID <- NULL + + plot_alignment <- match.arg(plot_alignment, + choices = c("horizontal", "vertical")) + + # ********data prepare********# + ## dimension reduction ## + dim_dfr <- get_dimReduction( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + reduction = "cells", + reduction_method = dim_reduction_to_use, + name = dim_reduction_name, + output = "data.table" + ) + dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use, dim3_to_use)] + dim_names <- colnames(dim_dfr) + dim_DT <- data.table::as.data.table(dim_dfr) + dim_DT[, cell_ID := rownames(dim_dfr)] + + + ## annotated cell metadata + cell_metadata <- combineMetadata( + gobject = gobject, + feat_type = feat_type, + spat_unit = spat_unit, + spat_enr_names = spat_enr_names + ) + annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") + spatial_locations <- getSpatialLocations( + gobject, + spat_unit = spat_unit, + name = spat_loc_name, + output = "data.table" + ) + if (is.null(spatial_locations)) { + return(NULL) + } + + annotated_DT <- merge(annotated_DT, spatial_locations, by = "cell_ID") + + + if (dim_reduction_to_use == "pca") { + pca_object <- get_dimReduction( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + reduction = "cells", + reduction_method = dim_reduction_to_use, + name = dim_reduction_name, + output = "dimObj" + ) + eigenvalues <- slot(pca_object, "misc")$eigenvalues + + if (!is.null(eigenvalues)) { + total <- sum(eigenvalues) + var_expl_vec <- (eigenvalues / total) * 100 + dim1_x_variance <- var_expl_vec[dim1_to_use] + dim2_y_variance <- var_expl_vec[dim2_to_use] + if (!is.null(dim3_to_use)) { + dim3_z_variance <- var_expl_vec[3] + } + } + } + + + + ## nn network + if (show_NN_network) { + # nn_network + selected_nn_network <- get_NearestNetwork( + gobject = gobject, + feat_type = feat_type, + spat_unit = spat_unit, + nn_network_to_use = nn_network_to_use, + network_name = network_name, + output = "igraph" + ) + network_DT <- data.table::as.data.table(igraph::as_data_frame( + selected_nn_network, what = "edges")) + + # annotated network + old_dim_names <- dim_names + + annotated_network_DT <- merge(network_DT, dim_DT, by.x = "from", + by.y = "cell_ID") + from_dim_names <- paste0("from_", old_dim_names) + data.table::setnames(annotated_network_DT, old = old_dim_names, + new = from_dim_names) + + annotated_network_DT <- merge(annotated_network_DT, dim_DT, + by.x = "to", by.y = "cell_ID") + to_dim_names <- paste0("to_", old_dim_names) + data.table::setnames(annotated_network_DT, old = old_dim_names, + new = to_dim_names) + } + + + + + ## extract spatial network + if (show_spatial_network == TRUE) { + spatial_network <- get_spatialNetwork(gobject, + spat_unit = spat_unit, + name = spatial_network_name, + output = "networkDT" + ) + } else { + spatial_network <- NULL + } + + + ## extract spatial grid + if (show_spatial_grid == TRUE) { + spatial_grid <- get_spatialGrid(gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spatial_grid_name + ) + } else { + spatial_grid <- NULL + } + + + # create matching cell_color_code + if (is.null(cell_color_code)) { + if (is.character(cell_color)) { + cell_metadata <- pDataDT(gobject, + feat_type = feat_type, + spat_unit = spat_unit + ) + if (cell_color %in% colnames(cell_metadata)) { + if (color_as_factor == TRUE) { + number_colors <- length(unique(cell_metadata[[cell_color]])) + cell_color_code <- set_default_color_discrete_cell( + instrs = instructions(gobject))(n = number_colors) + names(cell_color_code) <- unique( + cell_metadata[[cell_color]]) + } + } + } + } + + + ## subset cell selection ## + if (!is.null(select_cells) & !is.null(select_cell_groups)) { + if (is.null(cell_color)) { + stop("\n selection of cells is based on cell_color paramter, + which is a metadata column \n") + } + message("You have selected both individual cell IDs and a group + of cells") + group_cell_IDs <- annotated_DT[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + select_cells <- unique(c(select_cells, group_cell_IDs)) + } else if (!is.null(select_cell_groups)) { + select_cells <- annotated_DT[get(cell_color) %in% + select_cell_groups][["cell_ID"]] + } + + + if (!is.null(select_cells)) { + annotated_DT_other <- annotated_DT[!annotated_DT$cell_ID %in% + select_cells] + annotated_DT_selected <- annotated_DT[annotated_DT$cell_ID %in% + select_cells] + + if (show_NN_network == TRUE) { + annotated_network_DT <- annotated_network_DT[ + annotated_network_DT$to %in% select_cells & + annotated_network_DT$from %in% select_cells] + } + if (show_spatial_network == TRUE) { + spatial_network <- spatial_network[spatial_network$to %in% + select_cells & + spatial_network$from %in% + select_cells] + } + + # if specific cells are selected + # annotated_DT = annotated_DT_selected + } + + + ## if no subsets are required + if (is.null(select_cells) & is.null(select_cell_groups)) { + annotated_DT_selected <- annotated_DT + annotated_DT_other <- NULL + } + + ## annotated_DT_selected = all selected cells or all cells if no selection + ## annotated_DT_other = all not selected cells or NULL if no selection + + + + ########### dim plot ########### + # 2D plot + if (is.null(dim3_to_use)) { + dpl <- plotly::plot_ly() + if (show_NN_network == TRUE) { + if (is.null(nn_network_alpha)) { + nn_network_alpha <- 0.5 + } else if (is.character(nn_network_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + nn_network_alpha <- 0.5 + } + dpl <- dpl %>% plotly::add_segments( + name = network_name, + type = "scatter", + x = annotated_network_DT[[from_dim_names[1]]], + y = annotated_network_DT[[from_dim_names[2]]], + xend = annotated_network_DT[[to_dim_names[1]]], + yend = annotated_network_DT[[to_dim_names[2]]], + line = list( + color = nn_network_color, + width = 0.5 + ), + opacity = nn_network_alpha + ) + } + + if (is.null(cell_color)) { + # cell_color = "lightblue" + dpl <- dpl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_selected[[dim_names[1]]], + y = annotated_DT_selected[[dim_names[2]]], + # color = "lightblue", + # colors ="lightblue", + marker = list( + size = dim_point_size, + color = "lightblue" + ), + showlegend = FALSE + ) + } else if (cell_color %in% colnames(annotated_DT_selected)) { + if (color_as_factor) { + annotated_DT_selected[[cell_color]] <- as.factor( + annotated_DT_selected[[cell_color]]) + } + + + dpl <- dpl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_selected[[dim_names[1]]], + y = annotated_DT_selected[[dim_names[2]]], + color = annotated_DT_selected[[cell_color]], + colors = cell_color_code, + legendgroup = annotated_DT_selected[[cell_color]], + marker = list(size = dim_point_size) + ) + } else { + stop("cell_color does not exist!\n") + } + + + if ((show_cluster_center == TRUE | show_center_label == TRUE) & + !is.null(cell_color)) { + annotated_DT_centers <- annotated_DT_selected[, .( + center_1 = stats::median(get(dim_names[1])), + center_2 = stats::median(get(dim_names[2])) + ), + by = cell_color + ] + annotated_DT_centers[[cell_color]] <- as.factor( + annotated_DT_centers[[cell_color]]) + if (show_cluster_center == TRUE) { + dpl <- dpl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_centers[["center_1"]], + y = annotated_DT_centers[["center_2"]], + color = annotated_DT_centers[[cell_color]], + colors = cell_color_code, + legendgroup = annotated_DT_centers[[cell_color]], + marker = list(size = center_point_size, symbol = "x", + symbols = "x"), + showlegend = FALSE + ) + } + + if (show_center_label == TRUE) { + dpl <- dpl %>% plotly::add_text( + x = annotated_DT_centers[["center_1"]], + y = annotated_DT_centers[["center_2"]], + type = "scatter", mode = "text", + text = annotated_DT_centers[[cell_color]], + textposition = "middle right", + textfont = list( + color = "#000000", + size = label_size + ), + showlegend = FALSE + ) + } + } + if (show_other_cells == TRUE) { + dpl <- dpl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_other[[dim_names[1]]], + y = annotated_DT_other[[dim_names[2]]], + marker = list(size = other_point_size, + color = other_cell_color), + showlegend = FALSE + ) + } + if (dim_reduction_to_use == "pca") { + if (!is.null(eigenvalues)) { + x_name <- paste0("pca", "-", dim_names[1]) + y_name <- paste0("pca", "-", dim_names[2]) + x_title <- sprintf("%s explains %.02f%% of variance", + x_name, var_expl_vec[1]) + y_title <- sprintf("%s explains %.02f%% of variance", + y_name, var_expl_vec[2]) + } + } else { + x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") + y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") + } + dpl <- dpl %>% plotly::layout( + xaxis = list(title = x_title), + yaxis = list(title = y_title), + legend = list(x = 100, y = 0.5, + font = list(family = "sans-serif", + size = legend_text_size)) + ) + } + # 3D plot + else if (!is.null(dim3_to_use)) { + dpl <- plotly::plot_ly(scene = "scene1") + if (is.null(cell_color)) { + # cell_color = "lightblue" + dpl <- dpl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_selected[[dim_names[1]]], + y = annotated_DT_selected[[dim_names[2]]], + z = annotated_DT_selected[[dim_names[3]]], + color = "lightblue", + colors = "lightblue", + marker = list(size = dim_point_size), + showlegend = FALSE + ) + # legendgroup = annotated_DT_selected[[cell_color]]) + } else { + if (cell_color %in% colnames(annotated_DT_selected)) { + if (is.null(cell_color_code)) { + number_colors <- length(unique( + annotated_DT_selected[[cell_color]])) + cell_color_code <- set_default_color_discrete_cell( + instrs = instructions(gobject) + )(n = number_colors) + } + if (color_as_factor) { + annotated_DT_selected[[cell_color]] <- as.factor( + annotated_DT_selected[[cell_color]]) + } + dpl <- dpl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_selected[[dim_names[1]]], + y = annotated_DT_selected[[dim_names[2]]], + z = annotated_DT_selected[[dim_names[3]]], + color = annotated_DT_selected[[cell_color]], + colors = cell_color_code, + marker = list(size = dim_point_size), + legendgroup = annotated_DT_selected[[cell_color]] + ) + } else { + stop("cell_color does not exist!\n") + } + } + if (show_other_cells == TRUE) { + dpl <- dpl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_other[[dim_names[1]]], + y = annotated_DT_other[[dim_names[2]]], + z = annotated_DT_other[[dim_names[3]]], + marker = list(size = other_point_size, + color = other_cell_color), + showlegend = FALSE + ) + } + + if (show_NN_network) { + edges <- plotly_network( + annotated_network_DT, + "from_Dim.1", "from_Dim.2", "from_Dim.3", + "to_Dim.1", "to_Dim.2", "to_Dim.3" + ) + if (is.null(nn_network_alpha)) { + nn_network_alpha <- 0.5 + } else if (is.character(nn_network_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + nn_network_alpha <- 0.5 + } + + dpl <- dpl %>% plotly::add_trace( + name = network_name, + mode = "lines", + type = "scatter3d", + data = edges, + x = ~x, y = ~y, z = ~z, + line = list(color = nn_network_color), + opacity = nn_network_alpha + ) + } + if ((show_cluster_center == TRUE | show_center_label == TRUE) & + !is.null(cell_color)) { + annotated_DT_centers <- annotated_DT_selected[, .( + center_1 = stats::median(get(dim_names[1])), + center_2 = stats::median(get(dim_names[2])), + center_3 = stats::median(get(dim_names[3])) + ), + by = cell_color + ] + annotated_DT_centers[[cell_color]] <- as.factor( + annotated_DT_centers[[cell_color]]) + if (show_cluster_center == TRUE) { + dpl <- dpl %>% + plotly::add_trace( + mode = "markers", + type = "scatter3d", + data = annotated_DT_centers, + x = ~center_1, + y = ~center_2, + z = ~center_3, + color = annotated_DT_centers[[cell_color]], + colors = cell_color_code, + marker = list(size = 2, symbol = "x", symbols = "x"), + legendgroup = annotated_DT_centers[[cell_color]], + showlegend = FALSE + ) + } + if (show_center_label == TRUE) { + message(" center label is not clear to see in 3D plot. + You can shut it down with show_center_label = FALSE") + dpl <- dpl %>% + plotly::add_trace( + mode = "text", + type = "scatter3d", + data = annotated_DT_centers, + x = ~center_1, + y = ~center_2, + z = ~center_3, + text = annotated_DT_centers[[cell_color]], + legendgroup = annotated_DT_centers[[cell_color]], + showlegend = FALSE + ) + } + } + if (dim_reduction_to_use == "pca") { + x_name <- paste0("pca", "-", dim_names[1]) + y_name <- paste0("pca", "-", dim_names[2]) + z_name <- paste0("pca", "-", dim_names[3]) + x_title <- sprintf("%s explains %.02f%% of variance", + x_name, var_expl_vec[1]) + y_title <- sprintf("%s explains %.02f%% of variance", + y_name, var_expl_vec[2]) + z_title <- sprintf("%s explains %.02f%% of variance", + z_name, var_expl_vec[3]) + } else { + x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") + y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") + z_title <- paste(dim_reduction_to_use, dim_names[3], sep = " ") + } + } + + + + ############ spatial plot ########## + if (is.null(sdimx) | is.null(sdimy)) { + # cat('first and second dimension need to be defined, default is + # first 2 \n') + sdimx <- "sdimx" + sdimy <- "sdimy" + } + + ## 2D plot ## + if (is.null(sdimz)) { + spl <- plotly::plot_ly() + + if (show_spatial_network == TRUE) { + if (is.null(spatial_network)) { + stop("No usable spatial network specified! Please choose + a network with spatial_network_name=xxx") + } else { + if (is.null(spatial_network_alpha)) { + spatial_network_alpha <- 0.5 + } else if (is.character(spatial_network_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + spatial_network_alpha <- 0.5 + } + spl <- spl %>% plotly::add_segments( + name = spatial_network_name, + type = "scatter", + x = spatial_network[["sdimx_begin"]], + y = spatial_network[["sdimy_begin"]], + xend = spatial_network[["sdimx_end"]], + yend = spatial_network[["sdimy_end"]], + line = list( + color = spatial_network_color, + width = 0.5 + ), + opacity = spatial_network_alpha + ) + } + } + + + if (show_spatial_grid == TRUE) { + if (is.null(spatial_grid)) { + stop("No usable spatial grid specified! Please choose a + network with spatial_grid_name=xxx") + } else { + if (is.null(spatial_grid_color)) { + spatial_grid_color <- "black" + } + edges <- plotly_grid(spatial_grid) + spl <- spl %>% plotly::add_segments( + name = "spatial_grid", + type = "scatter", + data = edges, + x = ~x, + y = ~y, + xend = ~x_end, + yend = ~y_end, + line = list( + color = spatial_grid_color, + width = 1 + ), + opacity = spatial_grid_alpha + ) + } + } + if (is.null(cell_color)) { + # cell_color = "lightblue" + spl <- spl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_selected[[sdimx]], + y = annotated_DT_selected[[sdimy]], + # color = "lightblue", + # colors = "lightblue", + marker = list( + size = spatial_point_size, + color = "lightblue" + ), + showlegend = FALSE + ) + } else if (cell_color %in% colnames(annotated_DT_selected)) { + if (color_as_factor) { + annotated_DT_selected[[cell_color]] <- as.factor( + annotated_DT_selected[[cell_color]] + ) + } + + + spl <- spl %>% + plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_selected[[sdimx]], + y = annotated_DT_selected[[sdimy]], + color = annotated_DT_selected[[cell_color]], + colors = cell_color_code, + legendgroup = annotated_DT_selected[[cell_color]], + marker = list(size = spatial_point_size), + showlegend = FALSE + ) + } else { + stop("cell_color doesn't exist!\n") + } + if (show_other_cells == TRUE) { + spl <- spl %>% plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_other[[sdimx]], + y = annotated_DT_other[[sdimy]], + marker = list(size = other_point_size, + color = other_cell_color), + showlegend = FALSE + ) + } + spl <- spl %>% plotly::layout( + xaxis = list(title = "X"), + yaxis = list(title = "Y"), + legend = list(x = 100, y = 0.5, + font = list(family = "sans-serif", + size = legend_text_size)) + ) + } + + + ## 3D plot ## + else { + axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) + + ratio <- plotly_axis_scale_3D(annotated_DT_selected, + sdimx = sdimx, sdimy = sdimy, sdimz = sdimz, + mode = axis_scale, custom_ratio = custom_ratio + ) + spl <- plotly::plot_ly(scene = "scene2") + if (!is.null(cell_color)) { + if (cell_color %in% colnames(annotated_DT_selected)) { + annotated_DT_selected[[cell_color]] <- as.factor( + annotated_DT_selected[[cell_color]]) + spl <- spl %>% + plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_selected[[sdimx]], + y = annotated_DT_selected[[sdimy]], + z = annotated_DT_selected[[sdimz]], + color = annotated_DT_selected[[cell_color]], + colors = cell_color_code, + legendgroup = annotated_DT_selected[[cell_color]], + marker = list(size = spatial_point_size), + showlegend = FALSE + ) + } else { + stop("cell_color doesn't exist!\n") + } + } else { + spl <- spl %>% + plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_selected$sdimx, + y = annotated_DT_selected$sdimy, + z = annotated_DT_selected$sdimz, + color = "lightblue", + colors = "lightblue", + # legendgroup = annotated_DT_selected[[cell_color]], + marker = list(size = spatial_point_size), + showlegend = FALSE + ) + } + if (show_other_cells == TRUE) { + spl <- spl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_other[[sdimx]], + y = annotated_DT_other[[sdimy]], + z = annotated_DT_other[[sdimz]], + marker = list(size = other_point_size, + color = other_cell_color), + showlegend = FALSE + ) + } + if (show_spatial_network == TRUE) { + if (is.null(spatial_network)) { + stop("No usable spatial network specified! Please choose a + network with spatial_network_name=xxx") + } else { + if (is.null(spatial_network_alpha)) { + spatial_network_alpha <- 0.5 + } else if (is.character(spatial_network_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + spatial_network_alpha <- 0.5 + } + edges <- plotly_network(spatial_network) + + spl <- spl %>% plotly::add_trace( + name = "sptial network", + mode = "lines", + type = "scatter3d", + data = edges, + x = ~x, y = ~y, z = ~z, + line = list(color = spatial_network_color), + opacity = spatial_network_alpha + ) + } + } + + if (show_spatial_grid == TRUE) { + message("3D grid is not clear to view\n") + } + } + + + + + if (is.null(dim3_to_use) & is.null(sdimz)) { + if (plot_alignment == "vertical") { + combo_plot <- plotly::subplot(dpl, spl, nrows = 2, + titleX = TRUE, titleY = TRUE) + } else { + combo_plot <- plotly::subplot(dpl, spl, titleX = TRUE, + titleY = TRUE) + } + } else if (!is.null(dim3_to_use) & is.null(sdimz)) { + if (plot_alignment == "vertical") { + combo_plot <- plotly::subplot(dpl, spl, nrows = 2, titleX = TRUE, + titleY = TRUE) %>% + plotly::layout(scene = list( + domain = list(x = c(0, 1), y = c(0, 0.5)), + xaxis = list(title = x_title), + yaxis = list(title = y_title), + zaxis = list(title = z_title) + )) + } else { + combo_plot <- plotly::subplot(dpl, spl, titleX = TRUE, + titleY = TRUE) %>% + plotly::layout(scene = list( + domain = list(x = c(0, 0.5), y = c(0, 1)), + xaxis = list(title = x_title), + yaxis = list(title = y_title), + zaxis = list(title = z_title) + )) + } + } else if (is.null(dim3_to_use) & !is.null(sdimz)) { + if (plot_alignment == "vertical") { + combo_plot <- plotly::subplot(dpl, spl, nrows = 2, titleX = TRUE, + titleY = TRUE) %>% + plotly::layout(scene2 = list( + domain = list(x = c(0, 1), y = c(0.5, 1)), + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + )) + } else { + combo_plot <- plotly::subplot(dpl, spl, titleX = TRUE, + titleY = TRUE) %>% + plotly::layout(scene2 = list( + domain = list(x = c(0.5, 1), y = c(0, 1)), + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + )) + } + } else if (!is.null(dim3_to_use) & !is.null(sdimz)) { + if (plot_alignment == "vertical") { + combo_plot <- plotly::subplot(dpl, spl, nrows = 2, titleX = TRUE, + titleY = TRUE) %>% + plotly::layout( + scene = list( + domain = list(x = c(0, 1), y = c(0, 0.5)), + xaxis = list(title = x_title), + yaxis = list(title = y_title), + zaxis = list(title = z_title) + ), + scene2 = list( + domain = list(x = c(0, 1), y = c(0.5, 1)), + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ) + ) + } else { + combo_plot <- plotly::subplot(dpl, spl, titleX = TRUE, + titleY = TRUE) %>% + plotly::layout( + scene = list( + domain = list(x = c(0, 0.5), y = c(0, 1)), + xaxis = list(title = x_title), + yaxis = list(title = y_title), + zaxis = list(title = z_title) + ), + scene2 = list( + domain = list(x = c(0.5, 1), y = c(0, 1)), + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ) + ) + } + } + + show_plot <- ifelse(is.null(show_plot), + readGiottoInstructions(gobject, param = "show_plot"), + show_plot) + save_plot <- ifelse(is.null(save_plot), + readGiottoInstructions(gobject, param = "save_plot"), + save_plot) + return_plot <- ifelse(is.null(return_plot), + readGiottoInstructions(gobject, param = "return_plot"), + return_plot) + + ## print plot + if (show_plot == TRUE) { + print(combo_plot) + } + + ## save plot + if (save_plot == TRUE) { + do.call("all_plots_save_function", + c(list(gobject = gobject, plot_object = combo_plot, + default_save_name = default_save_name), save_param)) + } + + ## return plot + if (return_plot == TRUE) { + return(combo_plot) + } +} + + + + +# ** #### +# ** feature 3D plot #### + +#' @title spatFeatPlot3D +#' @name spatFeatPlot3D +#' @description Visualize cells and gene expression according to spatial +#' coordinates +#' @inheritParams data_access_params +#' @inheritParams plot_output_params +#' @param spat_loc_name name of spatial locations to use +#' @param expression_values gene expression values to use +#' @param feats feats to show +#' @param spat_enr_names names of spatial enrichment results to include +#' +#' @param cluster_column cluster column to select groups +#' @param select_cell_groups select subset of cells/clusters based on +#' cell_color parameter +#' @param select_cells select subset of cells based on cell IDs +#' @param show_other_cells display not selected cells +#' @param other_cell_color color of not selected cells +#' @param other_point_size size of not selected cells +#' +#' @param genes_high_color color represents high gene expression +#' @param genes_mid_color color represents middle gene expression +#' @param genes_low_color color represents low gene expression +#' @param show_network show underlying spatial network +#' @param network_color color of spatial network +#' @param spatial_network_name name of spatial network to use +#' @param edge_alpha alpha of edges +#' @param show_grid show spatial grid +#' @param spatial_grid_name name of spatial grid to use +#' +#' @param point_size size of point (cell) +#' @param show_legend show legend +#' +#' @param axis_scale the way to scale the axis +#' @param custom_ratio customize the scale of the plot +#' @param x_ticks set the number of ticks on the x-axis +#' @param y_ticks set the number of ticks on the y-axis +#' @param z_ticks set the number of ticks on the z-axis +#' @param ... additional params to pass +#' @family spatial gene expression visualizations +#' @returns plotly +#' @examples +#' g <- GiottoData::loadGiottoMini("starmap") +#' spatFeatPlot3D(g, feats = "Slc17a7") +#' +#' @export +spatFeatPlot3D <- function(gobject, + spat_unit = NULL, + feat_type = NULL, + spat_loc_name = "raw", + expression_values = c("normalized", "scaled", "custom"), + feats, + spat_enr_names = NULL, + show_network = FALSE, + network_color = NULL, + spatial_network_name = "Delaunay_network", + edge_alpha = NULL, + cluster_column = NULL, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = FALSE, + other_cell_color = "lightgrey", + other_point_size = 1, + genes_high_color = NULL, + genes_mid_color = "white", + genes_low_color = "blue", + show_grid = FALSE, + spatial_grid_name = "spatial_grid", + point_size = 2, + show_legend = TRUE, + axis_scale = c("cube", "real", "custom"), + custom_ratio = NULL, + x_ticks = NULL, + y_ticks = NULL, + z_ticks = NULL, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, + save_param = list(), + default_save_name = "spatFeatPlot3D", + ... +) { + + # Set feat_type and spat_unit + spat_unit <- set_default_spat_unit( + gobject = gobject, + spat_unit = spat_unit + ) + feat_type <- set_default_feat_type( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type + ) + + # data.table variables + cell_ID <- NULL + + selected_genes <- feats + + values <- match.arg(expression_values, c("normalized", "scaled", "custom")) + expr_values <- getExpression( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + values = values, + output = "matrix" + ) + + # only keep genes that are in the dataset + selected_genes <- selected_genes[selected_genes %in% rownames(expr_values)] + + # get selected feature expression values in data.table format + if (length(selected_genes) == 1) { + subset_expr_data <- expr_values[rownames(expr_values) %in% + selected_genes, ] + t_sub_expr_data_DT <- data.table::data.table( + "selected_gene" = subset_expr_data, + "cell_ID" = colnames(expr_values)) + data.table::setnames(t_sub_expr_data_DT, + "selected_gene", selected_genes) + } else { + subset_expr_data <- expr_values[rownames(expr_values) %in% + selected_genes, ] + t_sub_expr_data <- t_flex(subset_expr_data) + t_sub_expr_data_DT <- data.table::as.data.table( + as.matrix(t_sub_expr_data)) + t_sub_expr_data_DT[, cell_ID := rownames(t_sub_expr_data)] + } + + + ## extract cell locations + cell_locations <- getSpatialLocations( + gobject = gobject, + spat_unit = spat_unit, + name = spat_loc_name, + output = "data.table" + ) + if (is.null(cell_locations)) { + return(NULL) + } + + + ## extract spatial network + if (show_network == TRUE) { + spatial_network <- get_spatialNetwork(gobject, + spat_unit = spat_unit, + name = spatial_network_name, + output = "networkDT" + ) + } else { + spatial_network <- NULL + } + + ## extract spatial grid + if (show_grid == TRUE) { + spatial_grid <- get_spatialGrid(gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spatial_grid_name + ) + } else { + spatial_grid <- NULL + } + + ## extract cell metadata + cell_metadata <- try( + expr = combineMetadata( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spat_loc_name = spat_loc_name, + spat_enr_names = spat_enr_names + ), + silent = TRUE + ) + + + if (inherits(cell_metadata, "try-error")) { + cell_locations_metadata <- cell_locations + } else if (nrow(cell_metadata) == 0) { + cell_locations_metadata <- cell_locations + } else { + cell_locations_metadata <- cell_metadata + } + + + if (!is.null(select_cells) & !is.null(select_cell_groups)) { + message("You have selected both individual cell IDs and a group + of cells") + group_cell_IDs <- cell_locations_metadata[get(cluster_column) %in% + select_cell_groups][["cell_ID"]] + select_cells <- unique(c(select_cells, group_cell_IDs)) + } else if (!is.null(select_cell_groups)) { + select_cells <- cell_locations_metadata[get(cluster_column) %in% + select_cell_groups][["cell_ID"]] + } + + if (!is.null(select_cells)) { + cell_locations_metadata_other <- cell_locations_metadata[ + !cell_locations_metadata$cell_ID %in% select_cells] + cell_locations_metadata_selected <- cell_locations_metadata[ + cell_locations_metadata$cell_ID %in% select_cells] + spatial_network <- spatial_network[spatial_network$to %in% + select_cells & spatial_network$from %in% select_cells] + + # if specific cells are selected + cell_locations_metadata <- cell_locations_metadata_selected + } + + cell_locations_metadata_genes <- merge(cell_locations_metadata, + t_sub_expr_data_DT, by = "cell_ID") + + + + ## plotting ## + axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) + + ratio <- plotly_axis_scale_3D(cell_locations_metadata_genes, + sdimx = "sdimx", sdimy = "sdimy", sdimz = "sdimz", + mode = axis_scale, custom_ratio = custom_ratio + ) + + + ## spatial network data + if (!is.null(spatial_network) & show_network == TRUE) { + edges <- plotly_network(spatial_network) + } + + ## Point layer + if (length(selected_genes) > 4) { + stop("\n The max number of genes showed together is 4.Otherwise + it will be too small to see\n + \n If you have more genes to show, please divide them + into groups\n") + } + savelist <- list() + for (i in seq_len(length(selected_genes))) { + gene <- selected_genes[i] + if (!is.null(genes_high_color)) { + if (length(genes_high_color) != length(selected_genes) & + length(genes_high_color) != 1) { + stop("\n The number of genes and their corresbonding do + not match\n") + } else if (length(genes_high_color) == 1) { + genes_high_color <- rep(genes_high_color, + length(selected_genes)) + } + } else { + genes_high_color <- rep("red", length(selected_genes)) + } + pl <- plotly::plot_ly( + name = gene, + scene = paste("scene", i, sep = "") + ) %>% + plotly::add_trace( + data = cell_locations_metadata_genes, + type = "scatter3d", mode = "markers", + x = ~sdimx, y = ~sdimy, z = ~sdimz, + marker = list(size = point_size), + color = cell_locations_metadata_genes[[gene]], + colors = c(genes_low_color, genes_mid_color, + genes_high_color[i]) + ) + + if (show_other_cells == TRUE) { + pl <- pl %>% plotly::add_trace( + name = "unselected cells", + data = cell_locations_metadata_other, + type = "scatter3d", mode = "markers", + x = ~sdimx, y = ~sdimy, z = ~sdimz, + marker = list(size = other_point_size, color = other_cell_color) + ) + } + + + ## plot spatial network + if (show_network == TRUE) { + if (is.null(network_color)) { + network_color <- "lightblue" + } + if (is.null(edge_alpha)) { + edge_alpha <- 0.5 + } else if (is.character(edge_alpha)) { + edge_alpha <- 0.5 + message("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set") + } + pl <- pl %>% plotly::add_trace( + name = "sptial network", + mode = "lines", + type = "scatter3d", + data = edges, + x = ~x, y = ~y, z = ~z, + line = list(color = network_color, width = 0.5), + opacity = edge_alpha, + showlegend = FALSE + ) + } + + + ## plot spatial grid + if (!is.null(spatial_grid) & show_grid == TRUE) { + message("spatial grid is not clear in 3D plot") + } + + pl <- pl %>% plotly::colorbar(title = gene) + savelist[[gene]] <- pl + } + + + if (length(savelist) == 1) { + cowplot <- savelist[[1]] %>% plotly::layout(scene = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + )) + } else if (length(savelist) == 2) { + cowplot <- plotly::subplot(savelist) %>% + plotly::layout( + scene = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + scene2 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + # annotations = annotations, + legend = list(x = 100, y = 0) + ) + } else if (length(savelist) == 3) { + cowplot <- plotly::subplot(savelist) %>% + plotly::layout( + scene = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + scene2 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + scene3 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + legend = list(x = 100, y = 0) + ) + } else if (length(savelist) == 4) { + cowplot <- plotly::subplot(savelist) %>% + plotly::layout( + scene = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + scene2 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + scene3 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + scene4 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ), + legend = list(x = 100, y = 0) + ) + } + + + show_plot <- ifelse(is.null(show_plot), + readGiottoInstructions(gobject, param = "show_plot"), + show_plot) + save_plot <- ifelse(is.null(save_plot), + readGiottoInstructions(gobject, param = "save_plot"), + save_plot) + return_plot <- ifelse(is.null(return_plot), + readGiottoInstructions(gobject, param = "return_plot"), + return_plot) + ## print plot + if (show_plot == TRUE) { + print(cowplot) + } + + ## save plot + if (save_plot == TRUE) { + do.call("all_plots_save_function", + c(list(gobject = gobject, plot_object = cowplot, + default_save_name = default_save_name), save_param)) + } + + ## return plot + if (return_plot == TRUE) { + return(cowplot) + } +} + +#' @describeIn spatFeatPlot3D deprecated +#' @export +spatGenePlot3D <- function(...) { + deprecate_warn( + when = "0.2.0", + what = "spatGenePlot3D()", + with = "spatFeatPlot3D()" + ) + spatFeatPlot3D(...) +} + + +#' @title dimFeatPlot3D +#' @name dimFeatPlot3D +#' @description Visualize cells and gene expression according to +#' dimension reduction coordinates +#' @inheritParams data_access_params +#' @inheritParams plot_output_params +#' @param expression_values gene expression values to use +#' @param genes genes to show +#' @param dim_reduction_to_use dimension reduction to use +#' @param dim_reduction_name dimension reduction name +#' @param dim1_to_use dimension to use on x-axis +#' @param dim2_to_use dimension to use on y-axis +#' @param dim3_to_use dimension to use on z-axis +#' +#' @param show_NN_network show underlying NN network +#' @param nn_network_to_use type of NN network to use (kNN vs sNN) +#' @param network_name name of NN network to use, if show_NN_network = TRUE +#' @param network_color color of NN network +#' +#' @param cluster_column cluster column to select groups +#' @param select_cell_groups select subset of cells/clusters based on +#' cell_color parameter +#' @param select_cells select subset of cells based on cell IDs +#' @param show_other_cells display not selected cells +#' @param other_cell_color color of not selected cells +#' @param other_point_size size of not selected cells +#' +#' @param edge_alpha column to use for alpha of the edges +#' @param point_size size of point (cell) +#' +#' @param genes_high_color color for high expression levels +#' @param genes_mid_color color for medium expression levels +#' @param genes_low_color color for low expression levels +#' +#' @param show_legend show legend +#' @details Description of parameters. +#' @family dimension reduction gene expression visualizations +#' @returns plotly +#' @examples +#' g <- GiottoData::loadGiottoMini("starmap") +#' +#' dimFeatPlot3D(g, genes = "Slc17a7", dim_reduction_name = "3D_umap") +#' @export +dimFeatPlot3D <- function( + gobject, + feat_type = NULL, + spat_unit = NULL, + expression_values = c("normalized", "scaled", "custom"), + genes = NULL, + dim_reduction_to_use = "umap", + dim_reduction_name = "umap", + dim1_to_use = 1, + dim2_to_use = 2, + dim3_to_use = 3, + show_NN_network = FALSE, + nn_network_to_use = "sNN", + network_name = "sNN.pca", + network_color = "lightgray", + cluster_column = NULL, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = TRUE, + other_cell_color = "lightgrey", + other_point_size = 1, + edge_alpha = NULL, + point_size = 2, + genes_high_color = NULL, + genes_mid_color = "white", + genes_low_color = "blue", + show_legend = TRUE, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, + save_param = list(), + default_save_name = "dimFeatPlot3D") { + # Set feat_type and spat_unit + spat_unit <- set_default_spat_unit( + gobject = gobject, + spat_unit = spat_unit + ) + feat_type <- set_default_feat_type( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type + ) + + ## select genes ## + selected_genes <- genes + values <- match.arg(expression_values, c("normalized", "scaled", "custom")) + expr_values <- getExpression( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + values = values, + output = "matrix" + ) + + # only keep genes that are in the dataset + selected_genes <- selected_genes[selected_genes %in% rownames(expr_values)] + + # + if (length(selected_genes) == 1) { + subset_expr_data <- expr_values[ + rownames(expr_values) %in% selected_genes, ] + t_sub_expr_data_DT <- data.table::data.table( + "selected_gene" = subset_expr_data, + "cell_ID" = colnames(expr_values)) + data.table::setnames( + t_sub_expr_data_DT, "selected_gene", selected_genes) + } else { + subset_expr_data <- expr_values[ + rownames(expr_values) %in% selected_genes, ] + t_sub_expr_data <- t_flex(subset_expr_data) + t_sub_expr_data_DT <- data.table::as.data.table( + as.matrix(t_sub_expr_data)) + + # data.table variables + cell_ID <- NULL + + t_sub_expr_data_DT[, cell_ID := rownames(t_sub_expr_data)] + } + + + ## dimension reduction ## + dim_dfr <- getDimReduction(gobject, + reduction = "cells", + reduction_method = dim_reduction_to_use, + name = dim_reduction_name, + output = "data.table" + ) + dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use, dim3_to_use)] + dim_names <- colnames(dim_dfr) + dim_DT <- data.table::as.data.table(dim_dfr) + dim_DT[, cell_ID := rownames(dim_dfr)] + + ## annotated cell metadata + cell_metadata <- pDataDT(gobject, + feat_type = feat_type, + spat_unit = spat_unit + ) + annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") + + + + # create input for network + if (show_NN_network == TRUE) { + # nn_network + selected_nn_network <- getNearestNetwork( + gobject = gobject, + feat_type = feat_type, + spat_unit = spat_unit, + nn_type = nn_network_to_use, + name = network_name, + output = "igraph" + ) + network_DT <- data.table::as.data.table(igraph::as_data_frame( + selected_nn_network, what = "edges")) + + # annotated network + old_dim_names <- dim_names + + annotated_network_DT <- merge( + network_DT, dim_DT, by.x = "from", by.y = "cell_ID") + from_dim_names <- paste0("from_", old_dim_names) + data.table::setnames(annotated_network_DT, old = old_dim_names, + new = from_dim_names) + + annotated_network_DT <- merge( + annotated_network_DT, dim_DT, by.x = "to", by.y = "cell_ID") + to_dim_names <- paste0("to_", old_dim_names) + data.table::setnames(annotated_network_DT, old = old_dim_names, + new = to_dim_names) + } + + + ## create subsets if needed + if (!is.null(select_cells) & !is.null(select_cell_groups)) { + if (is.null(cluster_column)) { + stop("\n selection of cells is based on cell_color paramter, + which is a metadata column \n") + } + message("You have selected both individual cell IDs and a group + of cells") + group_cell_IDs <- annotated_DT[get(cluster_column) %in% + select_cell_groups][["cell_ID"]] + select_cells <- unique(c(select_cells, group_cell_IDs)) + } else if (!is.null(select_cell_groups)) { + select_cells <- annotated_DT[get(cluster_column) %in% + select_cell_groups][["cell_ID"]] + } + + if (!is.null(select_cells)) { + annotated_DT_other <- annotated_DT[ + !annotated_DT$cell_ID %in% select_cells] + annotated_DT_selected <- annotated_DT[ + annotated_DT$cell_ID %in% select_cells] + + if (show_NN_network == TRUE) { + annotated_network_DT <- annotated_network_DT[ + annotated_network_DT$to %in% select_cells & + annotated_network_DT$from %in% select_cells] + } + + # if specific cells are selected + annotated_DT <- annotated_DT_selected + } + + ## if no subsets are required + if (is.null(select_cells) & is.null(select_cell_groups)) { + annotated_DT_selected <- annotated_DT + annotated_DT_other <- NULL + } + + ## merge gene info + annotated_gene_DT <- merge(annotated_DT, t_sub_expr_data_DT, by = "cell_ID") + + + + ## visualize multipe plots ## + ## 3D plots ## + + + if (show_NN_network == TRUE) { + edges <- plotly_network( + annotated_network_DT, + "from_Dim.1", "from_Dim.2", "from_Dim.3", + "to_Dim.1", "to_Dim.2", "to_Dim.3" + ) + } + ## Point layer + if (length(selected_genes) > 4) { + stop("\n The max number of genes showed together is 4.Otherwise + it will be too small to see\n + \n If you have more genes to show, please divide them into + groups\n") + } + if (!is.null(genes_high_color)) { + if (length(genes_high_color) != length(selected_genes) & + length(genes_high_color) != 1) { + stop("\n The number of genes and their corresbonding do not + match\n") + } + } else if (is.null(genes_high_color)) { + genes_high_color <- rep("red", length(selected_genes)) + } else { + genes_high_color <- rep(genes_high_color, length(selected_genes)) + } + + titleX <- title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") + titleY <- title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") + titleZ <- title <- paste(dim_reduction_to_use, dim_names[3], sep = " ") + savelist <- list() + for (i in seq_len(length(selected_genes))) { + gene <- selected_genes[i] + + pl <- plotly::plot_ly(name = gene, scene = paste("scene", i, sep = "")) + pl <- pl %>% plotly::add_trace( + data = annotated_gene_DT, type = "scatter3d", mode = "markers", + x = annotated_gene_DT[[dim_names[1]]], + y = annotated_gene_DT[[dim_names[2]]], + z = annotated_gene_DT[[dim_names[3]]], + color = annotated_gene_DT[[gene]], + colors = c(genes_low_color, genes_mid_color, genes_high_color[i]), + marker = list(size = point_size) + ) + if (show_other_cells == TRUE) { + pl <- pl %>% plotly::add_trace( + name = "unselected cells", + data = annotated_DT_other, + type = "scatter3d", mode = "markers", + x = annotated_DT_other[[dim_names[1]]], + y = annotated_DT_other[[dim_names[2]]], + z = annotated_DT_other[[dim_names[3]]], + marker = list(size = other_point_size, color = other_cell_color) + ) + } + + ## plot spatial network + if (show_NN_network == TRUE) { + pl <- pl %>% plotly::add_trace( + name = "sptial network", mode = "lines", + type = "scatter3d", opacity = edge_alpha, + showlegend = FALSE, + data = edges, + x = ~x, y = ~y, z = ~z, + line = list( + color = network_color, + width = 0.5 + ) + ) + } + pl <- pl %>% plotly::colorbar(title = gene) + savelist[[gene]] <- pl + } + + if (length(savelist) == 1) { + cowplot <- savelist[[1]] %>% plotly::layout(scene = list( + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + )) + } else if (length(savelist) == 2) { + cowplot <- plotly::subplot( + savelist, titleX = TRUE, titleY = TRUE) %>% + plotly::layout( + scene = list( + domain = list(x = c(0, 0.5), y = c(0, 1)), + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + ), + scene2 = list( + domain = list(x = c(0.5, 1), y = c(0, 1)), + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + ), + legend = list(x = 100, y = 0) + ) + } else if (length(savelist) == 3) { + cowplot <- plotly::subplot( + savelist, titleX = TRUE, titleY = TRUE) %>% + plotly::layout( + scene = list( + domain = list(x = c(0, 0.5), y = c(0, 0.5)), + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + ), + scene2 = list( + domain = list(x = c(0.5, 1), y = c(0, 0.5)), + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + ), + scene3 = list( + domain = list(x = c(0, 0.5), y = c(0.5, 1)), + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + ), + legend = list(x = 100, y = 0) + ) + } else if (length(savelist) == 4) { + cowplot <- plotly::subplot(savelist) %>% + plotly::layout( + scene = list( + domain = list(x = c(0, 0.5), y = c(0, 0.5)), + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + ), + scene2 = list( + domain = list(x = c(0.5, 1), y = c(0, 0.5)), + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + ), + scene3 = list( + domain = list(x = c(0, 0.5), y = c(0.5, 1)), + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + ), + scene4 = list( + domain = list(x = c(0.5, 1), y = c(0.5, 1)), + xaxis = list(title = titleX), + yaxis = list(title = titleY), + zaxis = list(title = titleZ) + ), + legend = list(x = 100, y = 0) + ) + } + + show_plot <- ifelse(is.null(show_plot), + readGiottoInstructions(gobject, param = "show_plot"), + show_plot) + save_plot <- ifelse(is.null(save_plot), + readGiottoInstructions(gobject, param = "save_plot"), + save_plot) + return_plot <- ifelse(is.null(return_plot), + readGiottoInstructions(gobject, param = "return_plot"), + return_plot) + ## print plot + if (show_plot == TRUE) { + print(cowplot) + } + + ## save plot + if (save_plot == TRUE) { + do.call("all_plots_save_function", + c(list(gobject = gobject, plot_object = cowplot, + default_save_name = default_save_name), save_param)) + } + + ## return plot + if (return_plot == TRUE) { + return(cowplot) + } +} + +#' @describeIn dimFeatPlot3D deprecated +#' @param ... additional params to pass +#' @export +dimGenePlot3D <- function(...) { + deprecate_warn( + when = "0.2.0", + what = "dimGenePlot3D()", + with = "dimFeatPlot3D()" + ) + dimFeatPlot3D(...) +} + + + +#' @title spatDimFeatPlot3D +#' @name spatDimFeatPlot3D +#' @description Visualize cells according to spatial AND dimension +#' reduction coordinates in ggplot mode +#' @inheritParams data_access_params +#' @inheritParams plot_output_params +#' @param spat_loc_name name of spatial locations to use +#' @param expression_values gene expression values to use +#' @param plot_alignment direction to align plot +#' @param dim_reduction_to_use dimension reduction to use +#' @param dim_reduction_name dimension reduction name +#' @param dim1_to_use dimension to use on x-axis +#' @param dim2_to_use dimension to use on y-axis +#' @param dim3_to_use dimension to use on z-axis +#' @param sdimx spatial dimension to use on x-axis +#' @param sdimy spatial dimension to use on y-axis +#' @param sdimz spatial dimension to use on z-axis +#' @param genes genes to show +#' +#' @param cluster_column cluster column to select groups +#' @param select_cell_groups select subset of cells/clusters based on +#' cell_color parameter +#' @param select_cells select subset of cells based on cell IDs +#' @param show_other_cells display not selected cells +#' @param other_cell_color color of not selected cells +#' @param other_point_size size of not selected cells +#' +#' @param dim_point_size dim reduction plot: point size +#' @param show_NN_network show underlying NN network +#' @param nn_network_to_use type of NN network to use (kNN vs sNN) +#' @param nn_network_color color of NN network +#' @param nn_network_alpha alpha of NN network +#' @param network_name name of NN network to use, if show_NN_network = TRUE +#' +#' @param label_size size of labels +#' @param genes_high_color color for high expression levels +#' @param genes_mid_color color for medium expression levels +#' @param genes_low_color color for low expression levels +#' +#' @param show_spatial_network show spatial network (boolean) +#' @param spatial_network_name name of spatial network to use +#' @param spatial_network_color color of spatial network +#' @param spatial_network_alpha alpha of spatial network +#' +#' @param show_spatial_grid show spatial grid (boolean) +#' @param spatial_grid_name name of spatial grid to use +#' @param spatial_grid_color color of spatial grid +#' @param spatial_grid_alpha alpha of spatial grid +#' +#' @param spatial_point_size spatial plot: point size +#' @param legend_text_size size of legend +#' +#' @param axis_scale the way to scale the axis +#' @param custom_ratio customize the scale of the plot +#' @param x_ticks set the number of ticks on the x-axis +#' @param y_ticks set the number of ticks on the y-axis +#' @param z_ticks set the number of ticks on the z-axis +#' @details Description of parameters. +#' @family spatial and dimension reduction gene expression visualizations +#' @returns plotly +#' @examples +#' g <- GiottoData::loadGiottoMini("starmap") +#' spatDimFeatPlot3D(g, genes = "Slc17a7") +#' +#' @export +spatDimFeatPlot3D <- function(gobject, + feat_type = NULL, + spat_unit = NULL, + spat_loc_name = NULL, + expression_values = c("normalized", "scaled", "custom"), + plot_alignment = c("horizontal", "vertical"), + dim_reduction_to_use = "umap", + dim_reduction_name = "umap", + dim1_to_use = 1, + dim2_to_use = 2, + dim3_to_use = NULL, + sdimx = "sdimx", + sdimy = "sdimy", + sdimz = "sdimz", + genes, + cluster_column = NULL, + select_cell_groups = NULL, + select_cells = NULL, + show_other_cells = TRUE, + other_cell_color = "lightgrey", + other_point_size = 1.5, + show_NN_network = FALSE, + nn_network_to_use = "sNN", + nn_network_color = "lightgrey", + nn_network_alpha = 0.5, + network_name = "sNN.pca", + label_size = 16, + genes_low_color = "blue", + genes_mid_color = "white", + genes_high_color = "red", + dim_point_size = 3, + show_spatial_network = FALSE, + spatial_network_name = "Delaunay_network", + spatial_network_color = "lightgray", + spatial_network_alpha = 0.5, + show_spatial_grid = FALSE, + spatial_grid_name = "spatial_grid", + spatial_grid_color = NULL, + spatial_grid_alpha = 0.5, + spatial_point_size = 3, + legend_text_size = 12, + axis_scale = c("cube", "real", "custom"), + custom_ratio = NULL, + x_ticks = NULL, + y_ticks = NULL, + z_ticks = NULL, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, + save_param = list(), + default_save_name = "spatDimFeatPlot3D") { + # Set feat_type and spat_unit + spat_unit <- set_default_spat_unit( + gobject = gobject, + spat_unit = spat_unit + ) + feat_type <- set_default_feat_type( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type + ) + + # data.table variables + cell_ID <- NULL + + plot_alignment <- match.arg(plot_alignment, + choices = c("horizontal", "vertical")) + + ########### data prepare ########### + ## select genes ## + if (length(genes) > 1) { + warning("\n Now 3D mode can just accept one gene, only the first + gene will be plot\n") + genes <- genes[1] + } + selected_genes <- genes + values <- match.arg(expression_values, c("normalized", "scaled", "custom")) + expr_values <- get_expression_values( + gobject = gobject, + spat_unit = spat_unit, + feat_type = feat_type, + values = values, + output = "matrix" + ) + + # only keep genes that are in the dataset + selected_genes <- selected_genes[selected_genes %in% rownames(expr_values)] + subset_expr_data <- expr_values[rownames(expr_values) %in% selected_genes, ] + t_sub_expr_data_DT <- data.table::data.table( + "selected_gene" = subset_expr_data, "cell_ID" = colnames(expr_values)) + data.table::setnames(t_sub_expr_data_DT, "selected_gene", selected_genes) + + + ## dimension reduction ## + dim_dfr <- get_dimReduction(gobject, + reduction = "cells", + reduction_method = dim_reduction_to_use, + name = dim_reduction_name, + output = "data.table" + ) + dim_dfr <- dim_dfr[, c(dim1_to_use, dim2_to_use, dim3_to_use)] + dim_names <- colnames(dim_dfr) + dim_DT <- data.table::as.data.table(dim_dfr) + dim_DT[, cell_ID := rownames(dim_dfr)] + + + ## annotated cell metadata + cell_metadata <- pDataDT(gobject, + feat_type = feat_type, + spat_unit = spat_unit + ) + cell_locations <- get_spatial_locations( + gobject = gobject, + spat_unit = spat_unit, + spat_loc_name = spat_loc_name, + output = "data.table" + ) + if (is.null(cell_locations)) { + return(NULL) + } + + annotated_DT <- merge(cell_metadata, dim_DT, by = "cell_ID") + annotated_DT <- merge(annotated_DT, cell_locations, by = "cell_ID") + annotated_DT <- merge(annotated_DT, t_sub_expr_data_DT, by = "cell_ID") + + + ## nn network + if (show_NN_network) { + # nn_network + selected_nn_network <- get_NearestNetwork( + gobject = gobject, + feat_type = feat_type, + spat_unit = spat_unit, + nn_network_to_use = nn_network_to_use, + network_name = network_name, + output = "igraph" + ) + network_DT <- data.table::as.data.table(igraph::as_data_frame( + selected_nn_network, what = "edges")) + + # annotated network + old_dim_names <- dim_names + + annotated_network_DT <- merge( + network_DT, dim_DT, by.x = "from", by.y = "cell_ID") + from_dim_names <- paste0("from_", old_dim_names) + data.table::setnames( + annotated_network_DT, old = old_dim_names, new = from_dim_names) + + annotated_network_DT <- merge(annotated_network_DT, dim_DT, + by.x = "to", by.y = "cell_ID") + to_dim_names <- paste0("to_", old_dim_names) + data.table::setnames( + annotated_network_DT, old = old_dim_names, new = to_dim_names) + } + + + ## extract spatial network + if (show_spatial_network == TRUE) { + spatial_network <- get_spatialNetwork(gobject, + spat_unit = spat_unit, + name = spatial_network_name, + output = "networkDT" + ) + } else { + spatial_network <- NULL + } + + ## extract spatial grid + if (show_spatial_grid == TRUE) { + spatial_grid <- get_spatialGrid(gobject, + spat_unit = spat_unit, + feat_type = feat_type, + spatial_grid_name + ) + } else { + spatial_grid <- NULL + } + + + ## select subset of cells ## + if (!is.null(select_cells) & !is.null(select_cell_groups)) { + if (is.null(cluster_column)) { + stop("\n selection of cells is based on cell_color paramter, + which is a metadata column \n") + } + message("You have selected both individual cell IDs and a group + of cells") + group_cell_IDs <- annotated_DT[get(cluster_column) %in% + select_cell_groups][["cell_ID"]] + select_cells <- unique(c(select_cells, group_cell_IDs)) + } else if (!is.null(select_cell_groups)) { + select_cells <- annotated_DT[get(cluster_column) %in% + select_cell_groups][["cell_ID"]] + } + + if (!is.null(select_cells)) { + annotated_DT_other <- annotated_DT[ + !annotated_DT$cell_ID %in% select_cells] + annotated_DT_selected <- annotated_DT[ + annotated_DT$cell_ID %in% select_cells] + + if (show_NN_network == TRUE) { + annotated_network_DT <- annotated_network_DT[ + annotated_network_DT$to %in% select_cells & + annotated_network_DT$from %in% select_cells] + } + if (show_spatial_network == TRUE) { + spatial_network <- spatial_network[ + spatial_network$to %in% select_cells & + spatial_network$from %in% select_cells] + } + + # if specific cells are selected + annotated_DT <- annotated_DT_selected + } + + ## if no subsets are required + if (is.null(select_cells) & is.null(select_cell_groups)) { + annotated_DT_selected <- annotated_DT + annotated_DT_other <- NULL + } + + + + + ########### dim plot ########### + # 2D plot + if (is.null(dim3_to_use)) { + dpl <- plotly::plot_ly() + if (show_NN_network == TRUE) { + if (is.null(nn_network_alpha)) { + nn_network_alpha <- 0.5 + } else if (is.character(nn_network_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + nn_network_alpha <- 0.5 + } + dpl <- dpl %>% plotly::add_segments( + name = network_name, + type = "scatter", + x = annotated_network_DT[[from_dim_names[1]]], + y = annotated_network_DT[[from_dim_names[2]]], + xend = annotated_network_DT[[to_dim_names[1]]], + yend = annotated_network_DT[[to_dim_names[2]]], + line = list( + color = nn_network_color, + width = 0.5 + ), + opacity = nn_network_alpha + ) + } + + dpl <- dpl %>% + plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT[[dim_names[1]]], + y = annotated_DT[[dim_names[2]]], + color = annotated_DT[[selected_genes]], + colors = c( + genes_low_color, genes_mid_color, + genes_high_color + ), + marker = list(size = dim_point_size), + showlegend = FALSE + ) + + if (show_other_cells == TRUE) { + dpl <- dpl %>% + plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_other[[dim_names[1]]], + y = annotated_DT_other[[dim_names[2]]], + marker = list( + size = other_point_size, + color = other_cell_color + ), + showlegend = FALSE + ) + } + + x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") + y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") + + dpl <- dpl %>% plotly::layout( + xaxis = list(title = x_title), + yaxis = list(title = y_title), + legend = list(x = 100, y = 0.5, + font = list(family = "sans-serif", + size = legend_text_size)) + ) + } + # 3D plot + else if (!is.null(dim3_to_use)) { + dpl <- plotly::plot_ly(scene = "scene1") + + dpl <- dpl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT[[dim_names[1]]], + y = annotated_DT[[dim_names[2]]], + z = annotated_DT[[dim_names[3]]], + color = annotated_DT[[selected_genes]], + colors = c(genes_low_color, genes_mid_color, genes_high_color), + marker = list(size = dim_point_size), + showlegend = FALSE + ) + # legendgroup = annotated_DT[[cell_color]]) + if (show_other_cells == TRUE) { + dpl <- dpl %>% plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_other[[dim_names[1]]], + y = annotated_DT_other[[dim_names[2]]], + z = annotated_DT_other[[dim_names[3]]], + marker = list(size = other_point_size, + color = other_cell_color), + showlegend = FALSE + ) + } + + if (show_NN_network) { + edges <- plotly_network( + annotated_network_DT, + "from_Dim.1", "from_Dim.2", "from_Dim.3", + "to_Dim.1", "to_Dim.2", "to_Dim.3" + ) + if (is.null(nn_network_alpha)) { + nn_network_alpha <- 0.5 + } else if (is.character(nn_network_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + nn_network_alpha <- 0.5 + } + + dpl <- dpl %>% plotly::add_trace( + name = network_name, + mode = "lines", + type = "scatter3d", + data = edges, + x = ~x, y = ~y, z = ~z, + line = list(color = nn_network_color), + opacity = nn_network_alpha + ) + } + + + x_title <- paste(dim_reduction_to_use, dim_names[1], sep = " ") + y_title <- paste(dim_reduction_to_use, dim_names[2], sep = " ") + z_title <- paste(dim_reduction_to_use, dim_names[3], sep = " ") + } + dpl <- dpl %>% plotly::colorbar(title = selected_genes) + + + ########### spatial plot ########### + if (is.null(sdimx) | is.null(sdimy)) { + # cat('first and second dimenion need to be defined, + # default is first 2 \n') + sdimx <- "sdimx" + sdimy <- "sdimy" + } + + # 2D plot + if (is.null(sdimz)) { + spl <- plotly::plot_ly() + + if (show_spatial_network == TRUE) { + if (is.null(spatial_network)) { + stop("No usable spatial network specified! Please choose a + network with spatial_network_name=xxx") + } else { + if (is.null(spatial_network_alpha)) { + spatial_network_alpha <- 0.5 + } else if (is.character(spatial_network_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + spatial_network_alpha <- 0.5 + } + spl <- spl %>% plotly::add_segments( + name = spatial_network_name, + type = "scatter", + x = spatial_network[["sdimx_begin"]], + y = spatial_network[["sdimy_begin"]], + xend = spatial_network[["sdimx_end"]], + yend = spatial_network[["sdimy_end"]], + line = list( + color = spatial_network_color, + width = 0.5 + ), + opacity = spatial_network_alpha + ) + } + } + if (show_spatial_grid == TRUE) { + if (is.null(spatial_grid)) { + stop("No usable spatial grid specified! Please choose a + network with spatial_grid_name=xxx") + } else { + if (is.null(spatial_grid_color)) { + spatial_grid_color <- "black" + } + edges <- plotly_grid(spatial_grid) + spl <- spl %>% plotly::add_segments( + name = "spatial_grid", + type = "scatter", + data = edges, + x = ~x, + y = ~y, + xend = ~x_end, + yend = ~y_end, + line = list( + color = spatial_grid_color, + width = 1 + ), + opacity = spatial_grid_alpha + ) + } + } + + spl <- spl %>% + plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT[[sdimx]], + y = annotated_DT[[sdimy]], + color = annotated_DT[[selected_genes]], + colors = c( + genes_low_color, genes_mid_color, + genes_high_color + ), + marker = list(size = spatial_point_size), + showlegend = FALSE + ) + if (show_other_cells == TRUE) { + spl <- spl %>% + plotly::add_trace( + type = "scatter", mode = "markers", + x = annotated_DT_other[[sdimx]], + y = annotated_DT_other[[sdimy]], + marker = list( + size = other_point_size, + color = other_cell_color + ), + showlegend = FALSE + ) + } + + spl <- spl %>% plotly::layout( + xaxis = list(title = "X"), + yaxis = list(title = "Y"), + legend = list(x = 100, y = 0.5, + font = list(family = "sans-serif", + size = legend_text_size)) + ) + } + + + # 3D plot + else { + axis_scale <- match.arg(axis_scale, c("cube", "real", "custom")) + ratio <- plotly_axis_scale_3D(annotated_DT, + sdimx = sdimx, sdimy = sdimy, sdimz = sdimz, + mode = axis_scale, custom_ratio = custom_ratio + ) + + + spl <- plotly::plot_ly(scene = "scene2") + + spl <- spl %>% + plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT[[sdimx]], + y = annotated_DT[[sdimy]], + z = annotated_DT[[sdimz]], + color = annotated_DT[[selected_genes]], + colors = c( + genes_low_color, genes_mid_color, + genes_high_color + ), + # legendgroup = annotated_DT[[cell_color]], + marker = list(size = spatial_point_size), + showlegend = FALSE + ) + if (show_other_cells == TRUE) { + spl <- spl %>% + plotly::add_trace( + type = "scatter3d", mode = "markers", + x = annotated_DT_other[[sdimx]], + y = annotated_DT_other[[sdimy]], + z = annotated_DT_other[[sdimz]], + marker = list( + size = other_point_size, + color = other_cell_color + ), + showlegend = FALSE + ) + } + + if (show_spatial_network == TRUE) { + if (is.null(spatial_network)) { + stop("No usable spatial network specified! Please choose a + network with spatial_network_name=xxx") + } else { + if (is.null(spatial_network_alpha)) { + spatial_network_alpha <- 0.5 + } else if (is.character(spatial_network_alpha)) { + warning("Edge_alpha for plotly mode is not adjustable yet. + Default 0.5 will be set\n") + spatial_network_alpha <- 0.5 + } + edges <- plotly_network(spatial_network) + + spl <- spl %>% plotly::add_trace( + name = "sptial network", + mode = "lines", + type = "scatter3d", + data = edges, + x = ~x, y = ~y, z = ~z, + line = list(color = spatial_network_color), + opacity = spatial_network_alpha + ) + } + } + + if (show_spatial_grid == TRUE) { + message("3D grid is not clear to view") + } + } + + + + spl <- plotly::hide_colorbar(spl) + if (is.null(dim3_to_use) & is.null(sdimz)) { + if (plot_alignment == "vertical") { + combo_plot <- plotly::subplot( + dpl, spl, nrows = 2, titleX = TRUE, titleY = TRUE) + } else { + combo_plot <- plotly::subplot( + dpl, spl, titleX = TRUE, titleY = TRUE) + } + } else if (!is.null(dim3_to_use) & is.null(sdimz)) { + if (plot_alignment == "vertical") { + combo_plot <- plotly::subplot( + dpl, spl, nrows = 2, titleX = TRUE, titleY = TRUE) %>% + plotly::layout(scene = list( + domain = list(x = c(0, 1), y = c(0, 0.5)), + xaxis = list(title = x_title), + yaxis = list(title = y_title), + zaxis = list(title = z_title) + )) + } else { + combo_plot <- plotly::subplot( + dpl, spl, titleX = TRUE, titleY = TRUE) %>% + plotly::layout(scene = list( + domain = list(x = c(0, 0.5), y = c(0, 1)), + xaxis = list(title = x_title), + yaxis = list(title = y_title), + zaxis = list(title = z_title) + )) + } + } else if (is.null(dim3_to_use) & !is.null(sdimz)) { + if (plot_alignment == "vertical") { + combo_plot <- plotly::subplot( + dpl, spl, nrows = 2, titleX = TRUE, titleY = TRUE) %>% + plotly::layout(scene2 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + )) + } else { + combo_plot <- plotly::subplot( + dpl, spl, titleX = TRUE, titleY = TRUE) %>% + plotly::layout(scene2 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + )) + } + } else if (!is.null(dim3_to_use) & !is.null(sdimz)) { + if (plot_alignment == "vertical") { + combo_plot <- plotly::subplot( + dpl, spl, nrows = 2, titleX = TRUE, titleY = TRUE) %>% + plotly::layout( + scene = list( + domain = list(x = c(0, 1), y = c(0, 0.5)), + xaxis = list(title = x_title), + yaxis = list(title = y_title), + zaxis = list(title = z_title) + ), + scene2 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ) + ) + } else { + combo_plot <- plotly::subplot( + dpl, spl, titleX = TRUE, titleY = TRUE) %>% + plotly::layout( + scene = list( + domain = list(x = c(0, 0.5), y = c(0, 1)), + xaxis = list(title = x_title), + yaxis = list(title = y_title), + zaxis = list(title = z_title) + ), + scene2 = list( + xaxis = list(title = "X", nticks = x_ticks), + yaxis = list(title = "Y", nticks = y_ticks), + zaxis = list(title = "Z", nticks = z_ticks), + aspectmode = "manual", + aspectratio = list( + x = ratio[[1]], + y = ratio[[2]], + z = ratio[[3]] + ) + ) + ) + } + } + + show_plot <- ifelse(is.null(show_plot), + readGiottoInstructions(gobject, param = "show_plot"), + show_plot) + save_plot <- ifelse(is.null(save_plot), + readGiottoInstructions(gobject, param = "save_plot"), + save_plot) + return_plot <- ifelse(is.null(return_plot), + readGiottoInstructions(gobject, param = "return_plot"), + return_plot) + + ## print plot + if (show_plot == TRUE) { + print(combo_plot) + } + + ## save plot + if (save_plot == TRUE) { + do.call("all_plots_save_function", + c(list(gobject = gobject, plot_object = combo_plot, + default_save_name = default_save_name), save_param)) + } + + ## return plot + if (return_plot == TRUE) { + return(combo_plot) + } +} + +#' @describeIn spatDimFeatPlot3D deprecated +#' @param ... additional params to pass +#' @export +spatDimGenePlot3D <- function(...) { + deprecate_warn( + when = "0.2.0", + what = "spatDimGenePlot3D()", + with = "spatDimFeatPlot3D()" + ) + spatDimFeatPlot3D(...) +} + + +