diff --git a/R/auxiliary_giotto.R b/R/auxiliary_giotto.R index 099eca928..b09798683 100644 --- a/R/auxiliary_giotto.R +++ b/R/auxiliary_giotto.R @@ -115,9 +115,9 @@ filterDistributions <- function(gobject, fill_color = 'lightblue', scale_axis = 'identity', axis_offset = 0, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'filterDistributions') { @@ -281,7 +281,7 @@ filterCombinations <- function(gobject, y_axis_offset = 0, show_plot = TRUE, return_plot = FALSE, - save_plot = NA, + save_plot = NULL, save_param = list(), default_save_name = 'filterCombinations') { diff --git a/R/clustering.R b/R/clustering.R index 0fc1f9f23..ba60d34a6 100644 --- a/R/clustering.R +++ b/R/clustering.R @@ -379,9 +379,9 @@ doGiottoClustree <- function(gobject, res_vector = NULL, res_seq = NULL, return_gobject = FALSE, - show_plot = NA, - save_plot = NA, - return_plot = NA, + show_plot = NULL, + save_plot = NULL, + return_plot = NULL, save_param = list(), default_save_name = "clustree", verbose = TRUE, diff --git a/R/cross_section.R b/R/cross_section.R index 6a1d9e768..10ec0fd70 100644 --- a/R/cross_section.R +++ b/R/cross_section.R @@ -882,7 +882,7 @@ insertCrossSectionGenePlot3D <- function( show_other_cells = F, axis_scale = c("cube", "real", "custom"), custom_ratio = NULL, - show_plot = NA, return_plot = NA, save_plot = NA, + show_plot = NULL, return_plot = NULL, save_plot = NULL, save_param = list(), default_save_name = "spatGenePlot3D_with_cross_section", ... diff --git a/R/dimension_reduction.R b/R/dimension_reduction.R index 461038333..8b1ba4666 100644 --- a/R/dimension_reduction.R +++ b/R/dimension_reduction.R @@ -1262,9 +1262,9 @@ screePlot = function(gobject, ncp = 100, ylim = c(0, 20), verbose = TRUE, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'screePlot', ...) { @@ -1486,9 +1486,9 @@ jackstrawPlot = function(gobject, iter = 10, threshold = 0.01, verbose = TRUE, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'jackstrawPlot') { @@ -1656,9 +1656,9 @@ signPCA <- function(gobject, jack_threshold = 0.01, jack_ylim = c(0, 1), verbose = TRUE, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'signPCA') { diff --git a/R/spatial_enrichment_visuals.R b/R/spatial_enrichment_visuals.R index 41179cba6..7ddfe2186 100644 --- a/R/spatial_enrichment_visuals.R +++ b/R/spatial_enrichment_visuals.R @@ -102,9 +102,9 @@ plotCellTypesFromEnrichment <- function(gobject = NULL, title = NULL, save_param = list(), default_save_name = 'cell_types_from_enrichment', - save_plot = NA, - show_plot = NA, - return_plot = NA){ + save_plot = NULL, + show_plot = NULL, + return_plot = NULL){ # guard clauses handled at first step downstream # therefore, omitting here. id_and_types = findCellTypesFromEnrichment(gobject = gobject, @@ -165,9 +165,9 @@ pieCellTypesFromEnrichment <- function(gobject = NULL, title = NULL, save_param = list(), default_save_name = 'cell_types_from_enrichment_pie', - save_plot = NA, - show_plot = NA, - return_plot = NA){ + save_plot = NULL, + show_plot = NULL, + return_plot = NULL){ # guard clauses handled one step downstream freq_table = findCellTypesFromEnrichment(gobject = gobject, diff --git a/R/spatial_genes.R b/R/spatial_genes.R index 144c6c5aa..691a70b3f 100644 --- a/R/spatial_genes.R +++ b/R/spatial_genes.R @@ -1976,9 +1976,9 @@ spatialDE <- function(gobject = NULL, sig_alpha = 0.5, unsig_alpha = 0.5, python_path = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'SpatialDE'){ @@ -2675,9 +2675,9 @@ showPattern2D <- function(gobject, grid_border_color = 'grey', show_legend = T, point_size = 1, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'showPattern2D') { @@ -2786,9 +2786,9 @@ showPattern3D <- function(gobject, x_ticks = NULL, y_ticks = NULL, z_ticks = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'showPattern3D') { @@ -2884,9 +2884,9 @@ showPatternGenes <- function(gobject, top_neg_genes = 5, point_size = 1, return_DT = FALSE, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'showPatternGenes') { @@ -3800,9 +3800,9 @@ heatmSpatialCorFeats = function(gobject, show_column_dend = F, show_row_names = F, show_column_names = F, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'heatmSpatialCorFeats', ...) { @@ -3916,9 +3916,9 @@ heatmSpatialCorGenes = function(...) { rankSpatialCorGroups = function(gobject, spatCorObject, use_clus_name = NULL, - show_plot = NA, + show_plot = NULL, return_plot = FALSE, - save_plot = NA, + save_plot = NULL, save_param = list(), default_save_name = 'rankSpatialCorGroups') { diff --git a/R/spatial_interaction_spot.R b/R/spatial_interaction_spot.R index f3d8031f5..5a6c3478a 100644 --- a/R/spatial_interaction_spot.R +++ b/R/spatial_interaction_spot.R @@ -1203,9 +1203,9 @@ plotICFSpot <- function(gobject, source_markers, ICF_features, cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotICFSpot') { @@ -1301,9 +1301,9 @@ plotCellProximityFeatSpot = function(gobject, zscores_column = c('cell_type', 'features'), direction = c('both', 'up', 'down'), cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotCellProximityFeats') { diff --git a/R/spatial_interaction_visuals.R b/R/spatial_interaction_visuals.R index 416ee95a3..aeffa0cec 100644 --- a/R/spatial_interaction_visuals.R +++ b/R/spatial_interaction_visuals.R @@ -18,9 +18,9 @@ cellProximityBarplot = function(gobject, min_orig_ints = 5, min_sim_ints = 5, p_val = 0.05, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'cellProximityBarplot') { @@ -84,9 +84,9 @@ cellProximityHeatmap = function(gobject, order_cell_types = T, color_breaks = NULL, color_names = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'cellProximityHeatmap') { @@ -206,9 +206,9 @@ cellProximityNetwork = function(gobject, node_size = 4, node_color_code = NULL, node_text_size = 6, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'cellProximityNetwork') { @@ -1130,9 +1130,9 @@ plotCellProximityFeats = function(gobject, zscores_column = c('cell_type', 'feats'), direction = c('both', 'up', 'down'), cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotCellProximityFeats') { @@ -1404,9 +1404,9 @@ plotCPF = function(gobject, zscores_column = c('cell_type', 'feats'), direction = c('both', 'up', 'down'), cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotCPG') { @@ -1454,9 +1454,9 @@ plotInteractionChangedFeats = function(gobject, source_markers, ICF_feats, cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotInteractionChangedFeats') { @@ -1545,9 +1545,9 @@ plotICF = function(gobject, source_markers, ICF_feats, cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotICF') { @@ -1601,9 +1601,9 @@ plotCombineInteractionChangedFeats <- function(gobject, facet_ncol = length(selected_feat_to_feat), facet_nrow = length(selected_interactions), colors = c('#9932CC', '#FF8C00'), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotCombineICF') { @@ -1727,9 +1727,9 @@ plotCombineICF <- function(gobject, facet_ncol = length(selected_feat_to_feat), facet_nrow = length(selected_interactions), colors = c('#9932CC', '#FF8C00'), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotCombineICF') { @@ -1792,9 +1792,9 @@ plotCombineCellCellCommunication <- function(gobject, facet_ncol = length(selected_LR), facet_nrow = length(selected_cell_LR), colors = c('#9932CC', '#FF8C00'), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotCombineCellCellCommunication') { @@ -1909,9 +1909,9 @@ plotCombineCCcom = function(gobject, facet_ncol = length(selected_LR), facet_nrow = length(selected_cell_LR), colors = c('#9932CC', '#FF8C00'), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotCombineCCcom') { @@ -1964,9 +1964,9 @@ plotCCcomHeatmap = function(gobject, aggl_method = c("ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid"), gradient_color = NULL, gradient_style = c('divergent', 'sequential'), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotCCcomHeatmap') { @@ -2076,9 +2076,9 @@ plotCCcomDotplot = function(gobject, aggl_method = c("ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid"), dot_color_gradient = NULL, gradient_style = c('divergent', 'sequential'), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotCCcomDotplot') { @@ -2208,9 +2208,9 @@ plotRankSpatvsExpr = function(gobject, xlims = NULL, ylims = NULL, selected_ranks = c(1, 10, 20), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotRankSpatvsExpr') { @@ -2365,9 +2365,9 @@ plotRecovery = function(gobject, expr_rnk_column = 'exprPI_rnk', spat_rnk_column = 'spatPI_rnk', ground_truth = c('spatial', 'expression'), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'plotRecovery') { @@ -2472,9 +2472,9 @@ cellProximitySpatPlot2D <- function(gobject, point_alpha_other = 0.3, point_other_border_col = 'lightgrey', point_other_border_stroke = 0.01, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'cellProximitySpatPlot2D') { if(is.null(interaction_name)) { @@ -2731,9 +2731,9 @@ cellProximitySpatPlot3D = function(gobject, x_ticks = NULL, y_ticks = NULL, z_ticks = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'cellProximitySpatPlot3D', ...) { diff --git a/R/variable_genes.R b/R/variable_genes.R index e97169ee1..6a570d7d7 100644 --- a/R/variable_genes.R +++ b/R/variable_genes.R @@ -3,9 +3,9 @@ .calc_cov_group_hvf = function(feat_in_cells_detected, nr_expression_groups = 20, zscore_threshold = 1, - show_plot = NA, - return_plot = NA, - save_plot = NA) { + show_plot = NULL, + return_plot = NULL, + save_plot = NULL) { # NSE vars cov_group_zscore <- cov <- selected <- mean_expr <- NULL @@ -48,9 +48,9 @@ .calc_cov_loess_hvf = function(feat_in_cells_detected, difference_in_cov = 0.1, - show_plot = NA, - return_plot = NA, - save_plot = NA) { + show_plot = NULL, + return_plot = NULL, + save_plot = NULL) { # NSE vars cov_diff <- pred_cov_feats <- selected <- NULL @@ -79,9 +79,9 @@ .calc_var_hvf = function(scaled_matrix, var_threshold = 1.5, var_number = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, use_parallel = FALSE) { # NSE vars @@ -269,9 +269,9 @@ calculateHVF <- function(gobject, random_subset = NULL, set_seed = TRUE, seed_number = 1234, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = 'HVFplot', return_gobject = TRUE) { diff --git a/man/calculateHVF.Rd b/man/calculateHVF.Rd index 9f0c3842d..7b08086ab 100644 --- a/man/calculateHVF.Rd +++ b/man/calculateHVF.Rd @@ -22,9 +22,9 @@ calculateHVF( random_subset = NULL, set_seed = TRUE, seed_number = 1234, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "HVFplot", return_gobject = TRUE diff --git a/man/cellProximityBarplot.Rd b/man/cellProximityBarplot.Rd index 2220a5fd5..34f06b02a 100644 --- a/man/cellProximityBarplot.Rd +++ b/man/cellProximityBarplot.Rd @@ -10,9 +10,9 @@ cellProximityBarplot( min_orig_ints = 5, min_sim_ints = 5, p_val = 0.05, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "cellProximityBarplot" ) diff --git a/man/cellProximityHeatmap.Rd b/man/cellProximityHeatmap.Rd index 2202bdd0c..b7f5f8ef2 100644 --- a/man/cellProximityHeatmap.Rd +++ b/man/cellProximityHeatmap.Rd @@ -11,9 +11,9 @@ cellProximityHeatmap( order_cell_types = T, color_breaks = NULL, color_names = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "cellProximityHeatmap" ) diff --git a/man/cellProximityNetwork.Rd b/man/cellProximityNetwork.Rd index 317ce7328..1b3855fd4 100644 --- a/man/cellProximityNetwork.Rd +++ b/man/cellProximityNetwork.Rd @@ -20,9 +20,9 @@ cellProximityNetwork( node_size = 4, node_color_code = NULL, node_text_size = 6, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "cellProximityNetwork" ) diff --git a/man/cellProximitySpatPlot2D.Rd b/man/cellProximitySpatPlot2D.Rd index 0f7d82735..a4603d8da 100644 --- a/man/cellProximitySpatPlot2D.Rd +++ b/man/cellProximitySpatPlot2D.Rd @@ -33,9 +33,9 @@ cellProximitySpatPlot2D( point_alpha_other = 0.3, point_other_border_col = "lightgrey", point_other_border_stroke = 0.01, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "cellProximitySpatPlot2D" ) diff --git a/man/cellProximitySpatPlot3D.Rd b/man/cellProximitySpatPlot3D.Rd index dc7ba05d6..94285aaaa 100644 --- a/man/cellProximitySpatPlot3D.Rd +++ b/man/cellProximitySpatPlot3D.Rd @@ -31,9 +31,9 @@ cellProximitySpatPlot3D( x_ticks = NULL, y_ticks = NULL, z_ticks = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "cellProximitySpatPlot3D", ... diff --git a/man/doGiottoClustree.Rd b/man/doGiottoClustree.Rd index d26f07906..56743e14b 100644 --- a/man/doGiottoClustree.Rd +++ b/man/doGiottoClustree.Rd @@ -9,9 +9,9 @@ doGiottoClustree( res_vector = NULL, res_seq = NULL, return_gobject = FALSE, - show_plot = NA, - save_plot = NA, - return_plot = NA, + show_plot = NULL, + save_plot = NULL, + return_plot = NULL, save_param = list(), default_save_name = "clustree", verbose = TRUE, diff --git a/man/filterCombinations.Rd b/man/filterCombinations.Rd index 07c5a87cf..8613fe0fb 100644 --- a/man/filterCombinations.Rd +++ b/man/filterCombinations.Rd @@ -18,7 +18,7 @@ filterCombinations( y_axis_offset = 0, show_plot = TRUE, return_plot = FALSE, - save_plot = NA, + save_plot = NULL, save_param = list(), default_save_name = "filterCombinations" ) diff --git a/man/filterDistributions.Rd b/man/filterDistributions.Rd index 45fbf6dc5..22c69c7ba 100644 --- a/man/filterDistributions.Rd +++ b/man/filterDistributions.Rd @@ -18,9 +18,9 @@ filterDistributions( fill_color = "lightblue", scale_axis = "identity", axis_offset = 0, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "filterDistributions" ) diff --git a/man/heatmSpatialCorFeats.Rd b/man/heatmSpatialCorFeats.Rd index 06e4d39e6..3f58210e4 100644 --- a/man/heatmSpatialCorFeats.Rd +++ b/man/heatmSpatialCorFeats.Rd @@ -13,9 +13,9 @@ heatmSpatialCorFeats( show_column_dend = F, show_row_names = F, show_column_names = F, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "heatmSpatialCorFeats", ... diff --git a/man/insertCrossSectionGenePlot3D.Rd b/man/insertCrossSectionGenePlot3D.Rd index 4c558df6a..0e7bbc28c 100644 --- a/man/insertCrossSectionGenePlot3D.Rd +++ b/man/insertCrossSectionGenePlot3D.Rd @@ -19,9 +19,9 @@ insertCrossSectionGenePlot3D( show_other_cells = F, axis_scale = c("cube", "real", "custom"), custom_ratio = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "spatGenePlot3D_with_cross_section", ... diff --git a/man/jackstrawPlot.Rd b/man/jackstrawPlot.Rd index 7cea0f404..513bea377 100644 --- a/man/jackstrawPlot.Rd +++ b/man/jackstrawPlot.Rd @@ -18,9 +18,9 @@ jackstrawPlot( iter = 10, threshold = 0.01, verbose = TRUE, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "jackstrawPlot" ) diff --git a/man/pieCellTypesFromEnrichment.Rd b/man/pieCellTypesFromEnrichment.Rd index 1f515fba8..05c0819f0 100644 --- a/man/pieCellTypesFromEnrichment.Rd +++ b/man/pieCellTypesFromEnrichment.Rd @@ -12,9 +12,9 @@ pieCellTypesFromEnrichment( title = NULL, save_param = list(), default_save_name = "cell_types_from_enrichment_pie", - save_plot = NA, - show_plot = NA, - return_plot = NA + save_plot = NULL, + show_plot = NULL, + return_plot = NULL ) } \arguments{ diff --git a/man/plotCCcomDotplot.Rd b/man/plotCCcomDotplot.Rd index 8d3008a81..f10d959b5 100644 --- a/man/plotCCcomDotplot.Rd +++ b/man/plotCCcomDotplot.Rd @@ -17,9 +17,9 @@ plotCCcomDotplot( "median", "centroid"), dot_color_gradient = NULL, gradient_style = c("divergent", "sequential"), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotCCcomDotplot" ) diff --git a/man/plotCCcomHeatmap.Rd b/man/plotCCcomHeatmap.Rd index 68df8038c..89d134cc3 100644 --- a/man/plotCCcomHeatmap.Rd +++ b/man/plotCCcomHeatmap.Rd @@ -17,9 +17,9 @@ plotCCcomHeatmap( "median", "centroid"), gradient_color = NULL, gradient_style = c("divergent", "sequential"), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotCCcomHeatmap" ) diff --git a/man/plotCPF.Rd b/man/plotCPF.Rd index 0130a81ff..be9ef5516 100644 --- a/man/plotCPF.Rd +++ b/man/plotCPF.Rd @@ -19,9 +19,9 @@ plotCPF( zscores_column = c("cell_type", "feats"), direction = c("both", "up", "down"), cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotCPG" ) diff --git a/man/plotCellProximityFeatSpot.Rd b/man/plotCellProximityFeatSpot.Rd index 3591c8ce1..425bcef5e 100644 --- a/man/plotCellProximityFeatSpot.Rd +++ b/man/plotCellProximityFeatSpot.Rd @@ -18,9 +18,9 @@ plotCellProximityFeatSpot( zscores_column = c("cell_type", "features"), direction = c("both", "up", "down"), cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotCellProximityFeats" ) diff --git a/man/plotCellProximityFeats.Rd b/man/plotCellProximityFeats.Rd index 35479441e..226891e49 100644 --- a/man/plotCellProximityFeats.Rd +++ b/man/plotCellProximityFeats.Rd @@ -19,9 +19,9 @@ plotCellProximityFeats( zscores_column = c("cell_type", "feats"), direction = c("both", "up", "down"), cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotCellProximityFeats" ) diff --git a/man/plotCellTypesFromEnrichment.Rd b/man/plotCellTypesFromEnrichment.Rd index cd8b05510..ea53ee20f 100644 --- a/man/plotCellTypesFromEnrichment.Rd +++ b/man/plotCellTypesFromEnrichment.Rd @@ -12,9 +12,9 @@ plotCellTypesFromEnrichment( title = NULL, save_param = list(), default_save_name = "cell_types_from_enrichment", - save_plot = NA, - show_plot = NA, - return_plot = NA + save_plot = NULL, + show_plot = NULL, + return_plot = NULL ) } \arguments{ diff --git a/man/plotCombineCCcom.Rd b/man/plotCombineCCcom.Rd index 09657e7c2..472f9dccf 100644 --- a/man/plotCombineCCcom.Rd +++ b/man/plotCombineCCcom.Rd @@ -16,9 +16,9 @@ plotCombineCCcom( facet_ncol = length(selected_LR), facet_nrow = length(selected_cell_LR), colors = c("#9932CC", "#FF8C00"), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotCombineCCcom" ) diff --git a/man/plotCombineCellCellCommunication.Rd b/man/plotCombineCellCellCommunication.Rd index 493b3e66b..9140dd2c5 100644 --- a/man/plotCombineCellCellCommunication.Rd +++ b/man/plotCombineCellCellCommunication.Rd @@ -16,9 +16,9 @@ plotCombineCellCellCommunication( facet_ncol = length(selected_LR), facet_nrow = length(selected_cell_LR), colors = c("#9932CC", "#FF8C00"), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotCombineCellCellCommunication" ) diff --git a/man/plotCombineICF.Rd b/man/plotCombineICF.Rd index bf47a757f..da979a53e 100644 --- a/man/plotCombineICF.Rd +++ b/man/plotCombineICF.Rd @@ -16,9 +16,9 @@ plotCombineICF( facet_ncol = length(selected_feat_to_feat), facet_nrow = length(selected_interactions), colors = c("#9932CC", "#FF8C00"), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotCombineICF" ) diff --git a/man/plotCombineInteractionChangedFeats.Rd b/man/plotCombineInteractionChangedFeats.Rd index ba163fbf8..c01b8bedc 100644 --- a/man/plotCombineInteractionChangedFeats.Rd +++ b/man/plotCombineInteractionChangedFeats.Rd @@ -16,9 +16,9 @@ plotCombineInteractionChangedFeats( facet_ncol = length(selected_feat_to_feat), facet_nrow = length(selected_interactions), colors = c("#9932CC", "#FF8C00"), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotCombineICF" ) diff --git a/man/plotICF.Rd b/man/plotICF.Rd index 3d52defdc..b2d8725ed 100644 --- a/man/plotICF.Rd +++ b/man/plotICF.Rd @@ -11,9 +11,9 @@ plotICF( source_markers, ICF_feats, cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotICF" ) diff --git a/man/plotICFSpot.Rd b/man/plotICFSpot.Rd index d44309e41..6f75b56cb 100644 --- a/man/plotICFSpot.Rd +++ b/man/plotICFSpot.Rd @@ -11,9 +11,9 @@ plotICFSpot( source_markers, ICF_features, cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotICFSpot" ) diff --git a/man/plotInteractionChangedFeats.Rd b/man/plotInteractionChangedFeats.Rd index 23f0ccea1..66e85d3f0 100644 --- a/man/plotInteractionChangedFeats.Rd +++ b/man/plotInteractionChangedFeats.Rd @@ -11,9 +11,9 @@ plotInteractionChangedFeats( source_markers, ICF_feats, cell_color_code = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotInteractionChangedFeats" ) diff --git a/man/plotRankSpatvsExpr.Rd b/man/plotRankSpatvsExpr.Rd index 9740c45ee..24da8192d 100644 --- a/man/plotRankSpatvsExpr.Rd +++ b/man/plotRankSpatvsExpr.Rd @@ -17,9 +17,9 @@ plotRankSpatvsExpr( xlims = NULL, ylims = NULL, selected_ranks = c(1, 10, 20), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotRankSpatvsExpr" ) diff --git a/man/plotRecovery.Rd b/man/plotRecovery.Rd index fcd26502b..bb3698c0d 100644 --- a/man/plotRecovery.Rd +++ b/man/plotRecovery.Rd @@ -10,9 +10,9 @@ plotRecovery( expr_rnk_column = "exprPI_rnk", spat_rnk_column = "spatPI_rnk", ground_truth = c("spatial", "expression"), - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "plotRecovery" ) diff --git a/man/rankSpatialCorGroups.Rd b/man/rankSpatialCorGroups.Rd index dbe51874b..b6e834d5a 100644 --- a/man/rankSpatialCorGroups.Rd +++ b/man/rankSpatialCorGroups.Rd @@ -8,9 +8,9 @@ rankSpatialCorGroups( gobject, spatCorObject, use_clus_name = NULL, - show_plot = NA, + show_plot = NULL, return_plot = FALSE, - save_plot = NA, + save_plot = NULL, save_param = list(), default_save_name = "rankSpatialCorGroups" ) diff --git a/man/screePlot.Rd b/man/screePlot.Rd index 001ac5720..e6cc731a6 100644 --- a/man/screePlot.Rd +++ b/man/screePlot.Rd @@ -19,9 +19,9 @@ screePlot( ncp = 100, ylim = c(0, 20), verbose = TRUE, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "screePlot", ... diff --git a/man/showPattern2D.Rd b/man/showPattern2D.Rd index aa5e524a6..7fb3438c6 100644 --- a/man/showPattern2D.Rd +++ b/man/showPattern2D.Rd @@ -13,9 +13,9 @@ showPattern2D( grid_border_color = "grey", show_legend = T, point_size = 1, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "showPattern2D" ) diff --git a/man/showPattern3D.Rd b/man/showPattern3D.Rd index d0731de6d..589fc1729 100644 --- a/man/showPattern3D.Rd +++ b/man/showPattern3D.Rd @@ -18,9 +18,9 @@ showPattern3D( x_ticks = NULL, y_ticks = NULL, z_ticks = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "showPattern3D" ) diff --git a/man/showPatternGenes.Rd b/man/showPatternGenes.Rd index a8081a436..dfd346784 100644 --- a/man/showPatternGenes.Rd +++ b/man/showPatternGenes.Rd @@ -12,9 +12,9 @@ showPatternGenes( top_neg_genes = 5, point_size = 1, return_DT = FALSE, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "showPatternGenes" ) diff --git a/man/signPCA.Rd b/man/signPCA.Rd index 6bed10882..2e1f6132e 100644 --- a/man/signPCA.Rd +++ b/man/signPCA.Rd @@ -23,9 +23,9 @@ signPCA( jack_threshold = 0.01, jack_ylim = c(0, 1), verbose = TRUE, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "signPCA" ) diff --git a/man/spatialDE.Rd b/man/spatialDE.Rd index 595d36477..91ec9b013 100644 --- a/man/spatialDE.Rd +++ b/man/spatialDE.Rd @@ -15,9 +15,9 @@ spatialDE( sig_alpha = 0.5, unsig_alpha = 0.5, python_path = NULL, - show_plot = NA, - return_plot = NA, - save_plot = NA, + show_plot = NULL, + return_plot = NULL, + save_plot = NULL, save_param = list(), default_save_name = "SpatialDE" )