diff --git a/R/slot_accessors.R b/R/slot_accessors.R index ea49f966..fa70fd05 100644 --- a/R/slot_accessors.R +++ b/R/slot_accessors.R @@ -208,6 +208,7 @@ read_s4_nesting <- function(x) { #' setters for this slot directly retrieve (get) or replace (set) this slot. #' @seealso set_cell_id #' @keywords internal +#' @noRd get_cell_id <- function(gobject, spat_unit = NULL, set_defaults = TRUE) { @@ -251,6 +252,7 @@ get_cell_id <- function(gobject, #' on the giotto object. #' @seealso get_cell_id #' @keywords internal +#' @noRd set_cell_id <- function(gobject, spat_unit = NULL, cell_IDs, @@ -331,6 +333,7 @@ set_cell_id <- function(gobject, #' @seealso set_feat_id #' @family functions to set data in giotto object #' @keywords internal +#' @noRd get_feat_id <- function(gobject, feat_type = NULL, set_defaults = TRUE) { @@ -380,6 +383,7 @@ get_feat_id <- function(gobject, #' @seealso get_feat_id #' @family functions to set data in giotto object #' @keywords internal +#' @noRd set_feat_id <- function(gobject, feat_type = NULL, feat_IDs, @@ -581,7 +585,7 @@ set_feat_id <- function(gobject, #' @keywords internal #' @description Get cell metadata from giotto object #' @returns a data.table or cellMetaObj -#' @seealso pDataDT +#' @noRd get_cell_metadata <- function(gobject, spat_unit = NULL, feat_type = NULL, @@ -775,6 +779,7 @@ setCellMetadata <- function(gobject, #' @param verbose be verbose #' @returns giotto object #' @keywords internal +#' @noRd set_cell_metadata <- function(gobject, metadata, spat_unit = NULL, @@ -1001,6 +1006,7 @@ set_cell_metadata <- function(gobject, #' @returns a data.table or featMetaObj #' @seealso fDataDT #' @keywords internal +#' @noRd get_feature_metadata <- function(gobject, spat_unit = NULL, feat_type = NULL, @@ -1183,6 +1189,7 @@ setFeatureMetadata <- function(gobject, #' @param verbose be verbose #' @returns giotto object #' @keywords internal +#' @noRd set_feature_metadata <- function(gobject, metadata, spat_unit = NULL, @@ -1483,7 +1490,9 @@ getExpression <- function( #' @param output what object type to retrieve the expression as. Currently #' either matrix' for the matrix object contained in the exprObj or #' 'exprObj' (default) for the exprObj itself are allowed. +#' @keywords internal #' @returns exprObj or matrix depending on output param +#' @noRd get_expression_values <- function( gobject, spat_unit = NULL, @@ -1743,7 +1752,9 @@ setExpression <- function(gobject, #' @param verbose be verbose #' @param initialize (default = FALSE) whether to initialize the gobject before #' returning. Will be set to TRUE when called by the external +#' @keywords internal #' @returns giotto object +#' @noRd set_expression_values <- function(gobject, values, spat_unit = NULL, @@ -2236,6 +2247,7 @@ getSpatialLocations <- function(gobject, #' @param simplify logical. Whether or not to take object out of a list when #' there is a length of 1. #' @returns data.table with coordinates or spatLocsObj depending on \code{output} +#' @noRd get_spatial_locations <- function(gobject, spat_unit = NULL, spat_loc_name = NULL, @@ -2506,6 +2518,7 @@ setSpatialLocations <- function(gobject, #' the \code{spatLocsObj} will be nested by spat_unit 'nucleus' instead and #' its spat_unit slot will be changed to 'nucleus' #' @returns giotto object +#' @noRd set_spatial_locations <- function(gobject, spatlocs, spat_unit = NULL, @@ -2632,7 +2645,9 @@ set_spatial_locations <- function(gobject, #' @param output object type to return as. Either 'dimObj' (default) or 'matrix' #' of the embedding coordinates. #' @description Function to get a dimension reduction object +#' @keywords internal #' @returns dim reduction object (default) or dim reduction coordinates +#' @noRd get_dimReduction <- function(gobject, spat_unit = NULL, feat_type = NULL, @@ -2943,7 +2958,9 @@ setDimReduction <- function(gobject, #' @param dimObject dimension object result to set #' @param provenance provenance information (optional) #' @param verbose be verbose +#' @keywords internal #' @returns giotto object +#' @noRd set_dimReduction <- function(gobject, dimObject, spat_unit = NULL, @@ -3109,6 +3126,7 @@ set_dimReduction <- function(gobject, #' @param network_name name of NN network to be used #' @param output return a igraph or data.table object. Default 'igraph' #' @returns igraph or data.table object +#' @noRd get_NearestNetwork <- function(gobject, spat_unit = NULL, feat_type = NULL, @@ -3419,6 +3437,7 @@ setNearestNetwork <- function(gobject, #' @param verbose be verbose #' @returns giotto object #' @keywords internal +#' @noRd set_NearestNetwork <- function(gobject, nn_network, spat_unit = NULL, @@ -3568,6 +3587,7 @@ set_NearestNetwork <- function(gobject, #' @param simplify logical. Whether or not to take object out of a list when #' there is a length of 1. #' @returns spatialNetworkObj of data.table +#' @noRd get_spatialNetwork <- function(gobject, spat_unit = NULL, name = NULL, @@ -3913,6 +3933,7 @@ setSpatialNetwork <- function(gobject, #' @param spatial_network spatial network #' @param verbose be verbose #' @returns giotto object +#' @noRd set_spatialNetwork <- function(gobject, spatial_network, spat_unit = NULL, @@ -4033,6 +4054,7 @@ set_spatialNetwork <- function(gobject, #' @param name name of spatial grid #' @param return_grid_Obj return grid object (default = FALSE) #' @returns spatialGridObj +#' @noRd get_spatialGrid <- function(gobject, spat_unit = NULL, feat_type = NULL, @@ -4173,6 +4195,7 @@ getSpatialGrid <- function(gobject, #' @param name name of spatial grid #' @param verbose be verbose #' @returns giotto object +#' @noRd set_spatialGrid <- function(gobject, spatial_grid, spat_unit = NULL, @@ -4314,6 +4337,7 @@ setSpatialGrid <- function(gobject, #' @param simplify logical. Whether or not to take object out of a list when #' there is a length of 1. #' @returns spatVector +#' @noRd get_polygon_info <- function(gobject, polygon_name = NULL, polygon_overlap = NULL, @@ -4646,6 +4670,7 @@ setPolygonInfo <- function(gobject, #' @param gpolygon giottoPolygon object #' @param verbose be verbose #' @returns giotto object +#' @noRd set_polygon_info <- function(gobject, gpolygon, polygon_name = "cell", @@ -4843,6 +4868,7 @@ getFeatureInfo <- function(gobject = gobject, #' @description Get giotto points spatVector #' @returns a SpatVector (default) or giottoPoints object depending on value of #' return_giottoPoints +#' @noRd get_feature_info <- function(gobject, feat_type = NULL, set_defaults = TRUE, @@ -5023,6 +5049,7 @@ setFeatureInfo <- function(gobject, #' @param gpolygon typo do not use #' @param verbose be verbose #' @returns giotto object +#' @noRd set_feature_info <- function(gobject, gpoints, feat_type = NULL, @@ -5187,6 +5214,7 @@ set_feature_info <- function(gobject, #' @inheritParams data_access_params #' @param enrichm_name name of spatial enrichment results. Default "DWLS" #' @returns spatEnrObj or data.table with fractions +#' @noRd get_spatial_enrichment <- function(gobject, spat_unit = NULL, feat_type = NULL, @@ -5460,6 +5488,7 @@ setSpatialEnrichment <- function(gobject, #' @param provenance provenance information (optional) #' @param verbose be verbose #' @returns giotto object +#' @noRd set_spatial_enrichment <- function(gobject, spatenrichment, spat_unit = NULL, @@ -5596,6 +5625,7 @@ set_spatial_enrichment <- function(gobject, #' @param name name of giottoImage \code{\link{showGiottoImageNames}} #' @returns a giottoImage #' @keywords internal +#' @noRd get_giottoImage_MG <- function(gobject, name = NULL) { g_image_names <- list_images(gobject, img_type = "image") @@ -5629,6 +5659,7 @@ get_giottoImage_MG <- function(gobject, #' @param verbose be verbose #' @returns giotto object #' @keywords internal +#' @noRd set_giottoImage_MG <- function(gobject, image_object, name = NULL, @@ -5668,6 +5699,7 @@ set_giottoImage_MG <- function(gobject, #' @param name name of giottoLargeImage \code{\link{showGiottoImageNames}} #' @returns a giottoLargeImage #' @keywords internal +#' @noRd get_giottoLargeImage <- function(gobject, name = NULL) { g_image_names <- list_images(gobject, img_type = "largeImage") @@ -5701,6 +5733,7 @@ get_giottoLargeImage <- function(gobject, #' @param verbose be verbose #' @returns giotto object #' @keywords internal +#' @noRd set_giottoLargeImage <- function(gobject, largeImage_object, name = NULL, @@ -5742,6 +5775,7 @@ set_giottoLargeImage <- function(gobject, #' @param image_type deprecated #' @param name name of a giotto image object \code{\link{showGiottoImageNames}} #' @returns a giotto image object +#' @noRd get_giottoImage <- function(gobject = NULL, image_type = NULL, name = NULL) { @@ -5842,7 +5876,7 @@ get_giotto_image_list <- function(gobject, #' @param name name of giotto image object #' @param verbose be verbose #' @returns giotto object -#' @seealso \code{\link{addGiottoImage}} +#' @noRd set_giottoImage <- function(gobject = NULL, image = NULL, image_type = NULL, diff --git a/man/get_NearestNetwork.Rd b/man/get_NearestNetwork.Rd deleted file mode 100644 index e95b3d8d..00000000 --- a/man/get_NearestNetwork.Rd +++ /dev/null @@ -1,39 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_NearestNetwork} -\alias{get_NearestNetwork} -\title{Get nearest network} -\usage{ -get_NearestNetwork( - gobject, - spat_unit = NULL, - feat_type = NULL, - nn_network_to_use = NULL, - network_name = NULL, - output = c("nnNetObj", "igraph", "data.table"), - set_defaults = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{nn_network_to_use}{"kNN" or "sNN"} - -\item{network_name}{name of NN network to be used} - -\item{output}{return a igraph or data.table object. Default 'igraph'} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -igraph or data.table object -} -\description{ -Get a NN-network from a Giotto object -} diff --git a/man/get_cell_id.Rd b/man/get_cell_id.Rd deleted file mode 100644 index bf3dd4c7..00000000 --- a/man/get_cell_id.Rd +++ /dev/null @@ -1,30 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_cell_id} -\alias{get_cell_id} -\title{Get cell IDs for a given spatial unit} -\usage{ -get_cell_id(gobject, spat_unit = NULL, set_defaults = TRUE) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -character vector of cell_IDs -} -\description{ -Data for each spatial unit is expected to agree on a single -set of cell_IDs that are shared across any feature types. These cell_IDs -are stored within the giotto object's \code{cell_ID} slot. Getters and -setters for this slot directly retrieve (get) or replace (set) this slot. -} -\seealso{ -set_cell_id -} -\keyword{internal} diff --git a/man/get_cell_metadata.Rd b/man/get_cell_metadata.Rd deleted file mode 100644 index c4f708cb..00000000 --- a/man/get_cell_metadata.Rd +++ /dev/null @@ -1,41 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_cell_metadata} -\alias{get_cell_metadata} -\title{Get cell metadata} -\usage{ -get_cell_metadata( - gobject, - spat_unit = NULL, - feat_type = NULL, - output = c("cellMetaObj", "data.table"), - copy_obj = TRUE, - set_defaults = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{output}{return as either 'data.table' or 'cellMetaObj'} - -\item{copy_obj}{whether to deep copy/duplicate when getting the object -(default = TRUE)} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -a data.table or cellMetaObj -} -\description{ -Get cell metadata from giotto object -} -\seealso{ -pDataDT -} -\keyword{internal} diff --git a/man/get_dimReduction.Rd b/man/get_dimReduction.Rd deleted file mode 100644 index fcece087..00000000 --- a/man/get_dimReduction.Rd +++ /dev/null @@ -1,43 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_dimReduction} -\alias{get_dimReduction} -\title{Get dimension reduction} -\usage{ -get_dimReduction( - gobject, - spat_unit = NULL, - feat_type = NULL, - reduction = c("cells", "feats"), - reduction_method = NULL, - name = NULL, - output = c("dimObj", "matrix"), - set_defaults = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{reduction}{reduction on cells or features (e.g. "cells", "feats")} - -\item{reduction_method}{reduction method (e.g. "pca", "umap", "tsne")} - -\item{name}{name of reduction results} - -\item{output}{object type to return as. Either 'dimObj' (default) or 'matrix' -of the embedding coordinates.} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -dim reduction object (default) or dim reduction coordinates -} -\description{ -Function to get a dimension reduction object -} diff --git a/man/get_expression_values.Rd b/man/get_expression_values.Rd deleted file mode 100644 index 110a6d19..00000000 --- a/man/get_expression_values.Rd +++ /dev/null @@ -1,39 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_expression_values} -\alias{get_expression_values} -\title{get_expression_values} -\usage{ -get_expression_values( - gobject, - spat_unit = NULL, - feat_type = NULL, - values = c("raw", "normalized", "scaled"), - output = c("exprObj", "matrix"), - set_defaults = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{values}{expression values to -extract (e.g. "raw", "normalized", "scaled")} - -\item{output}{what object type to retrieve the expression as. Currently -either matrix' for the matrix object contained in the exprObj or -'exprObj' (default) for the exprObj itself are allowed.} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -exprObj or matrix depending on output param -} -\description{ -get_expression_values -} diff --git a/man/get_feat_id.Rd b/man/get_feat_id.Rd deleted file mode 100644 index c56ac215..00000000 --- a/man/get_feat_id.Rd +++ /dev/null @@ -1,49 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_feat_id} -\alias{get_feat_id} -\title{Get feat IDs for a given feature type} -\usage{ -get_feat_id(gobject, feat_type = NULL, set_defaults = TRUE) -} -\arguments{ -\item{gobject}{giotto object} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -character -} -\description{ -Across a single modality/feature type, all feature information -is expected to share a single set of feat_IDs. These feat_IDs are stored -within the giotto object's \code{feat_ID} slot. Getters and setters for this -slot directly (get) or replace (set) this slot. -} -\seealso{ -set_feat_id - -Other functions to set data in giotto object: -\code{\link{setCellMetadata}()}, -\code{\link{setDimReduction}()}, -\code{\link{setExpression}()}, -\code{\link{setFeatureInfo}()}, -\code{\link{setFeatureMetadata}()}, -\code{\link{setGiotto}()}, -\code{\link{setGiottoImage}()}, -\code{\link{setMultiomics}()}, -\code{\link{setNearestNetwork}()}, -\code{\link{setPolygonInfo}()}, -\code{\link{setSpatialEnrichment}()}, -\code{\link{setSpatialGrid}()}, -\code{\link{setSpatialLocations}()}, -\code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, -\code{\link{set_multiomics}()} -} -\concept{functions to set data in giotto object} -\keyword{internal} diff --git a/man/get_feature_info.Rd b/man/get_feature_info.Rd deleted file mode 100644 index d124327e..00000000 --- a/man/get_feature_info.Rd +++ /dev/null @@ -1,35 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_feature_info} -\alias{get_feature_info} -\title{Get feature info} -\usage{ -get_feature_info( - gobject, - feat_type = NULL, - set_defaults = TRUE, - return_giottoPoints = FALSE, - simplify = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{return_giottoPoints}{return as a giottoPoints object} - -\item{simplify}{logical. Whether or not to take object out of a list when -there is a length of 1.} -} -\value{ -a SpatVector (default) or giottoPoints object depending on value of -return_giottoPoints -} -\description{ -Get giotto points spatVector -} diff --git a/man/get_feature_metadata.Rd b/man/get_feature_metadata.Rd deleted file mode 100644 index 72f57c29..00000000 --- a/man/get_feature_metadata.Rd +++ /dev/null @@ -1,40 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_feature_metadata} -\alias{get_feature_metadata} -\title{Get feature metadata} -\usage{ -get_feature_metadata( - gobject, - spat_unit = NULL, - feat_type = NULL, - output = c("featMetaObj", "data.table"), - copy_obj = TRUE, - set_defaults = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{output}{return as either 'data.table' or 'featMetaObj'} - -\item{copy_obj}{whether to perform a deepcopy of the data.table information} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -a data.table or featMetaObj -} -\description{ -Get feature metadata from giotto object -} -\seealso{ -fDataDT -} -\keyword{internal} diff --git a/man/get_giottoImage.Rd b/man/get_giottoImage.Rd deleted file mode 100644 index 6bbde027..00000000 --- a/man/get_giottoImage.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_giottoImage} -\alias{get_giottoImage} -\title{Get giotto image object} -\usage{ -get_giottoImage(gobject = NULL, image_type = NULL, name = NULL) -} -\arguments{ -\item{gobject}{giotto object} - -\item{image_type}{deprecated} - -\item{name}{name of a giotto image object \code{\link{showGiottoImageNames}}} -} -\value{ -a giotto image object -} -\description{ -Get giotto image object from gobject -} diff --git a/man/get_giottoImage_MG.Rd b/man/get_giottoImage_MG.Rd deleted file mode 100644 index 3a28437c..00000000 --- a/man/get_giottoImage_MG.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_giottoImage_MG} -\alias{get_giottoImage_MG} -\title{Get \emph{magick}-based giotto \code{image}} -\usage{ -get_giottoImage_MG(gobject, name = NULL) -} -\arguments{ -\item{gobject}{giotto object} - -\item{name}{name of giottoImage \code{\link{showGiottoImageNames}}} -} -\value{ -a giottoImage -} -\description{ -Get a giottoImage from a giotto object -} -\keyword{internal} diff --git a/man/get_giottoLargeImage.Rd b/man/get_giottoLargeImage.Rd deleted file mode 100644 index bd3af696..00000000 --- a/man/get_giottoLargeImage.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_giottoLargeImage} -\alias{get_giottoLargeImage} -\title{Get \emph{terra}-based giotto \code{largeImage}} -\usage{ -get_giottoLargeImage(gobject, name = NULL) -} -\arguments{ -\item{gobject}{giotto object} - -\item{name}{name of giottoLargeImage \code{\link{showGiottoImageNames}}} -} -\value{ -a giottoLargeImage -} -\description{ -Set a giottoLargeImage from a giottoObject -} -\keyword{internal} diff --git a/man/get_polygon_info.Rd b/man/get_polygon_info.Rd deleted file mode 100644 index dbdd8286..00000000 --- a/man/get_polygon_info.Rd +++ /dev/null @@ -1,37 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_polygon_info} -\alias{get_polygon_info} -\title{Get polygon info} -\usage{ -get_polygon_info( - gobject, - polygon_name = NULL, - polygon_overlap = NULL, - return_giottoPolygon = FALSE, - verbose = TRUE, - simplify = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{polygon_name}{name of polygons. Default "cell"} - -\item{polygon_overlap}{if not NULL, return specified polygon overlap -information} - -\item{return_giottoPolygon}{(Defaults to FALSE) Return as giottoPolygon S4 -object} - -\item{verbose}{be verbose} - -\item{simplify}{logical. Whether or not to take object out of a list when -there is a length of 1.} -} -\value{ -spatVector -} -\description{ -Get giotto polygon spatVector -} diff --git a/man/get_spatialGrid.Rd b/man/get_spatialGrid.Rd deleted file mode 100644 index 5089f89b..00000000 --- a/man/get_spatialGrid.Rd +++ /dev/null @@ -1,36 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_spatialGrid} -\alias{get_spatialGrid} -\title{Get spatial grid} -\usage{ -get_spatialGrid( - gobject, - spat_unit = NULL, - feat_type = NULL, - name = NULL, - return_grid_Obj = FALSE, - set_defaults = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{name}{name of spatial grid} - -\item{return_grid_Obj}{return grid object (default = FALSE)} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -spatialGridObj -} -\description{ -Function to get spatial grid -} diff --git a/man/get_spatialNetwork.Rd b/man/get_spatialNetwork.Rd deleted file mode 100644 index e1b8e893..00000000 --- a/man/get_spatialNetwork.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_spatialNetwork} -\alias{get_spatialNetwork} -\title{Get spatial network} -\usage{ -get_spatialNetwork( - gobject, - spat_unit = NULL, - name = NULL, - output = c("spatialNetworkObj", "networkDT", "networkDT_before_filter", "outputObj"), - set_defaults = TRUE, - copy_obj = TRUE, - verbose = TRUE, - simplify = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{name}{name of spatial network} - -\item{output}{object type to return as. Options: -'spatialNetworkObj' (default), -'networkDT' and 'networkDT_before_filter' for data.table outputs.} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{copy_obj}{whether to copy/duplicate when getting the -object (default = TRUE)} - -\item{verbose}{be verbose} - -\item{simplify}{logical. Whether or not to take object out of a list when -there is a length of 1.} -} -\value{ -spatialNetworkObj of data.table -} -\description{ -Function to get a spatial network -} diff --git a/man/get_spatial_enrichment.Rd b/man/get_spatial_enrichment.Rd deleted file mode 100644 index 7dd0a1ac..00000000 --- a/man/get_spatial_enrichment.Rd +++ /dev/null @@ -1,40 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_spatial_enrichment} -\alias{get_spatial_enrichment} -\title{Get spatial enrichment} -\usage{ -get_spatial_enrichment( - gobject, - spat_unit = NULL, - feat_type = NULL, - enrichm_name = "DWLS", - output = c("spatEnrObj", "data.table"), - copy_obj = TRUE, - set_defaults = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{enrichm_name}{name of spatial enrichment results. Default "DWLS"} - -\item{output}{what format in which to get information (e.g. "data.table")} - -\item{copy_obj}{whether to deep copy/duplicate when getting the object -(default = TRUE)} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -spatEnrObj or data.table with fractions -} -\description{ -Function to get a spatial enrichment data.table -} diff --git a/man/get_spatial_locations.Rd b/man/get_spatial_locations.Rd deleted file mode 100644 index ac08e1e5..00000000 --- a/man/get_spatial_locations.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{get_spatial_locations} -\alias{get_spatial_locations} -\title{Get spatial locations} -\usage{ -get_spatial_locations( - gobject, - spat_unit = NULL, - spat_loc_name = NULL, - output = c("spatLocsObj", "data.table"), - copy_obj = TRUE, - verbose = TRUE, - set_defaults = TRUE, - simplify = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{spat_loc_name}{name of spatial -locations (defaults to first name in spatial_locs slot, e.g. "raw")} - -\item{output}{what object type to get the spatial locations as. Default is as -a 'spatLocsObj'. Returning as 'data.table' is also possible.} - -\item{copy_obj}{whether to copy/duplicate when getting the -object (default = TRUE)} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{simplify}{logical. Whether or not to take object out of a list when -there is a length of 1.} -} -\value{ -data.table with coordinates or spatLocsObj depending on \code{output} -} -\description{ -Function to get a spatial location data.table -} diff --git a/man/setCellMetadata.Rd b/man/setCellMetadata.Rd index c1740f5d..e534933d 100644 --- a/man/setCellMetadata.Rd +++ b/man/setCellMetadata.Rd @@ -52,7 +52,6 @@ setCellMetadata(gobject = g, x = createCellMetaObj(m2)) } \seealso{ Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, \code{\link{setFeatureInfo}()}, @@ -66,7 +65,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/setDimReduction.Rd b/man/setDimReduction.Rd index 9dd191e2..37818c2a 100644 --- a/man/setDimReduction.Rd +++ b/man/setDimReduction.Rd @@ -61,7 +61,6 @@ Other dimensional reduction data accessor functions: \code{\link{getDimReduction}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setExpression}()}, \code{\link{setFeatureInfo}()}, @@ -75,7 +74,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{dimensional reduction data accessor functions} diff --git a/man/setExpression.Rd b/man/setExpression.Rd index cf1344a3..cc7be0ea 100644 --- a/man/setExpression.Rd +++ b/man/setExpression.Rd @@ -58,7 +58,6 @@ Other expression accessor functions: \code{\link{getExpression}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setFeatureInfo}()}, @@ -72,7 +71,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{expression accessor functions} diff --git a/man/setFeatureInfo.Rd b/man/setFeatureInfo.Rd index 5710d4fd..b19037ac 100644 --- a/man/setFeatureInfo.Rd +++ b/man/setFeatureInfo.Rd @@ -45,7 +45,6 @@ Other feature info data accessor functions: \code{\link{getFeatureInfo}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -59,7 +58,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{feature info data accessor functions} diff --git a/man/setFeatureMetadata.Rd b/man/setFeatureMetadata.Rd index 8edceeb7..a7f8bf91 100644 --- a/man/setFeatureMetadata.Rd +++ b/man/setFeatureMetadata.Rd @@ -52,7 +52,6 @@ setFeatureMetadata(gobject = g, x = createFeatMetaObj(m2)) } \seealso{ Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -66,7 +65,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/setGiotto.Rd b/man/setGiotto.Rd index 93faebe6..67caab60 100644 --- a/man/setGiotto.Rd +++ b/man/setGiotto.Rd @@ -66,7 +66,6 @@ setGiotto(gobject = g, x = g_expression) } \seealso{ Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -80,7 +79,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/setGiottoImage.Rd b/man/setGiottoImage.Rd index b74e9f0c..15106fed 100644 --- a/man/setGiottoImage.Rd +++ b/man/setGiottoImage.Rd @@ -46,7 +46,6 @@ Other image data accessor functions: \code{\link{getGiottoImage}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -60,7 +59,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/setMultiomics.Rd b/man/setMultiomics.Rd index ef3d33eb..78d9a352 100644 --- a/man/setMultiomics.Rd +++ b/man/setMultiomics.Rd @@ -54,7 +54,6 @@ Other multiomics accessor functions: \code{\link{set_multiomics}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -68,7 +67,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/setNearestNetwork.Rd b/man/setNearestNetwork.Rd index ca1059d3..2ee260f4 100644 --- a/man/setNearestNetwork.Rd +++ b/man/setNearestNetwork.Rd @@ -58,7 +58,6 @@ Other expression space nearest network accessor functions: \code{\link{getNearestNetwork}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -72,7 +71,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{expression space nearest network accessor functions} diff --git a/man/setPolygonInfo.Rd b/man/setPolygonInfo.Rd index 4c405996..20aeb3cd 100644 --- a/man/setPolygonInfo.Rd +++ b/man/setPolygonInfo.Rd @@ -60,7 +60,6 @@ Other polygon info data accessor functions: \code{\link{getPolygonInfo}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -74,7 +73,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/setSpatialEnrichment.Rd b/man/setSpatialEnrichment.Rd index 1426738d..8b9ed631 100644 --- a/man/setSpatialEnrichment.Rd +++ b/man/setSpatialEnrichment.Rd @@ -54,7 +54,6 @@ Other spatial enrichment data accessor functions: \code{\link{getSpatialEnrichment}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -68,7 +67,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/setSpatialGrid.Rd b/man/setSpatialGrid.Rd index 9eb7886a..6d91c9fc 100644 --- a/man/setSpatialGrid.Rd +++ b/man/setSpatialGrid.Rd @@ -52,7 +52,6 @@ Other spatial grid data accessor functions: \code{\link{getSpatialGrid}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -66,7 +65,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialEnrichment}()}, \code{\link{setSpatialLocations}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/setSpatialLocations.Rd b/man/setSpatialLocations.Rd index c32e8eb2..44cf7c62 100644 --- a/man/setSpatialLocations.Rd +++ b/man/setSpatialLocations.Rd @@ -57,7 +57,6 @@ Other spatial location data accessor functions: \code{\link{getSpatialLocations}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -71,7 +70,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialEnrichment}()}, \code{\link{setSpatialGrid}()}, \code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/setSpatialNetwork.Rd b/man/setSpatialNetwork.Rd index 1c35d3a8..f1ddfd74 100644 --- a/man/setSpatialNetwork.Rd +++ b/man/setSpatialNetwork.Rd @@ -51,7 +51,6 @@ Other spatial network data accessor functions: \code{\link{getSpatialNetwork}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -65,7 +64,6 @@ Other functions to set data in giotto object: \code{\link{setSpatialEnrichment}()}, \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, -\code{\link{set_feat_id}()}, \code{\link{set_multiomics}()} } \concept{functions to set data in giotto object} diff --git a/man/set_NearestNetwork.Rd b/man/set_NearestNetwork.Rd deleted file mode 100644 index 9c1dffe3..00000000 --- a/man/set_NearestNetwork.Rd +++ /dev/null @@ -1,51 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_NearestNetwork} -\alias{set_NearestNetwork} -\title{Set nearest network} -\usage{ -set_NearestNetwork( - gobject, - nn_network, - spat_unit = NULL, - feat_type = NULL, - nn_network_to_use = "sNN", - network_name = "sNN.pca", - provenance = NULL, - verbose = TRUE, - set_defaults = TRUE, - initialize = FALSE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{nn_network}{nnNetObj or igraph nearest network object. Data.table not -yet supported.} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{nn_network_to_use}{"kNN" or "sNN"} - -\item{network_name}{name of NN network to be used} - -\item{provenance}{provenance information (optional)} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning} -} -\value{ -giotto object -} -\description{ -Set a NN-network for a Giotto object -} -\keyword{internal} diff --git a/man/set_cell_id.Rd b/man/set_cell_id.Rd deleted file mode 100644 index 581a2d5c..00000000 --- a/man/set_cell_id.Rd +++ /dev/null @@ -1,51 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_cell_id} -\alias{set_cell_id} -\title{Set cell IDs for a given spatial unit} -\usage{ -set_cell_id( - gobject, - spat_unit = NULL, - cell_IDs, - set_defaults = TRUE, - verbose = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{cell_IDs}{character vector of cell IDs to set. (See details)} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{verbose}{be verbose} -} -\value{ -giotto object with set cell_ID slot -} -\description{ -Setter function for the cell_ID slot. Directly replaces (sets) -this slot -} -\details{ -Data for each spatial unit is expected to agree on a single set of cell_IDs -that are shared across any feature types. These cell_IDs are stored within -the giotto object's \code{cell_ID} slot. \cr - -Pass \code{NULL} to \code{cell_IDs} param in order to delete the entry. \cr -Pass \code{'initialize'} to \code{cell_IDs} param in order to initialize the -specified entry. \cr - -\strong{NOTE:} The main purpose of the setter is to initialize, as cell_ID -values are AUTOMATICALLY updated every time \code{initialize()} is called -on the giotto object. -} -\seealso{ -get_cell_id -} -\keyword{internal} diff --git a/man/set_cell_metadata.Rd b/man/set_cell_metadata.Rd deleted file mode 100644 index 077a9a13..00000000 --- a/man/set_cell_metadata.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_cell_metadata} -\alias{set_cell_metadata} -\title{Set cell metadata} -\usage{ -set_cell_metadata( - gobject, - metadata, - spat_unit = NULL, - feat_type = NULL, - provenance = NULL, - verbose = TRUE, - set_defaults = TRUE, - initialize = FALSE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{metadata}{cellMetaObj or data.table containing cell metadata. -Setting NULL will remove the object. Passing 'initialize' will reset -the object.} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{provenance}{provenance information to set} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning} -} -\value{ -giotto object -} -\description{ -Function to set cell metadata information into giotto object -} -\keyword{internal} diff --git a/man/set_dimReduction.Rd b/man/set_dimReduction.Rd deleted file mode 100644 index ebd3948e..00000000 --- a/man/set_dimReduction.Rd +++ /dev/null @@ -1,52 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_dimReduction} -\alias{set_dimReduction} -\title{Set dimension reduction} -\usage{ -set_dimReduction( - gobject, - dimObject, - spat_unit = NULL, - feat_type = NULL, - reduction = c("cells", "feats"), - reduction_method = c("pca", "umap", "tsne"), - name = "pca", - provenance = NULL, - verbose = TRUE, - set_defaults = TRUE, - initialize = FALSE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{dimObject}{dimension object result to set} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{reduction}{reduction on cells or features} - -\item{reduction_method}{reduction method (e.g. "pca")} - -\item{name}{name of reduction results} - -\item{provenance}{provenance information (optional)} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning} -} -\value{ -giotto object -} -\description{ -Function to set a dimension reduction slot -} diff --git a/man/set_expression_values.Rd b/man/set_expression_values.Rd deleted file mode 100644 index 7483f84c..00000000 --- a/man/set_expression_values.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_expression_values} -\alias{set_expression_values} -\title{Set expression values} -\usage{ -set_expression_values( - gobject, - values, - spat_unit = NULL, - feat_type = NULL, - name = "test", - provenance = NULL, - verbose = TRUE, - set_defaults = TRUE, - initialize = FALSE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{values}{exprObj If NULL, then the object will be removed.} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{name}{name for the expression slot} - -\item{provenance}{provenance information (optional)} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning. Will be set to TRUE when called by the external} -} -\value{ -giotto object -} -\description{ -Function to set expression values for giotto object -} diff --git a/man/set_feat_id.Rd b/man/set_feat_id.Rd deleted file mode 100644 index b127d47c..00000000 --- a/man/set_feat_id.Rd +++ /dev/null @@ -1,71 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_feat_id} -\alias{set_feat_id} -\title{Set feat IDs for a given feature type} -\usage{ -set_feat_id( - gobject, - feat_type = NULL, - feat_IDs, - set_defaults = TRUE, - verbose = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{feat_IDs}{character vector of feature IDs to set.} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{verbose}{be verbose} -} -\value{ -giotto object with set cell_ID slot -} -\description{ -Setter function for the feat_ID slot. Directly replaces (sets) -this slot -} -\details{ -Across a single modality/feature type, and within a spatial unit, all feature -information is expected to share a single set of feat_IDs. These feat_IDs -are stored within the giotto object's \code{feat_ID} slot separated by -feat_type. \cr - -Pass \code{NULL} to \code{feat_IDs} param in order to delete the entry. \cr -Pass \code{'initialize'} to \code{feat_IDs} param in order to initialize the -specified entry. \cr - -\strong{NOTE:} The main purpose of the setter is to initialize, as feat_ID -values are AUTOMATICALLY updated every time \code{initialize()} is called on -the giotto object. -} -\seealso{ -get_feat_id - -Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, -\code{\link{setCellMetadata}()}, -\code{\link{setDimReduction}()}, -\code{\link{setExpression}()}, -\code{\link{setFeatureInfo}()}, -\code{\link{setFeatureMetadata}()}, -\code{\link{setGiotto}()}, -\code{\link{setGiottoImage}()}, -\code{\link{setMultiomics}()}, -\code{\link{setNearestNetwork}()}, -\code{\link{setPolygonInfo}()}, -\code{\link{setSpatialEnrichment}()}, -\code{\link{setSpatialGrid}()}, -\code{\link{setSpatialLocations}()}, -\code{\link{setSpatialNetwork}()}, -\code{\link{set_multiomics}()} -} -\concept{functions to set data in giotto object} -\keyword{internal} diff --git a/man/set_feature_info.Rd b/man/set_feature_info.Rd deleted file mode 100644 index d354e706..00000000 --- a/man/set_feature_info.Rd +++ /dev/null @@ -1,40 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_feature_info} -\alias{set_feature_info} -\title{Set feature info} -\usage{ -set_feature_info( - gobject, - gpoints, - feat_type = NULL, - verbose = TRUE, - set_defaults = TRUE, - initialize = FALSE, - gpolygon = NULL -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{gpoints}{giotto points object} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning} - -\item{gpolygon}{typo do not use} -} -\value{ -giotto object -} -\description{ -Set giotto polygon spatVector for features -} diff --git a/man/set_feature_metadata.Rd b/man/set_feature_metadata.Rd deleted file mode 100644 index 4cd28b6e..00000000 --- a/man/set_feature_metadata.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_feature_metadata} -\alias{set_feature_metadata} -\title{Set feature metadata} -\usage{ -set_feature_metadata( - gobject, - metadata, - spat_unit = NULL, - feat_type = NULL, - provenance = NULL, - verbose = TRUE, - set_defaults = TRUE, - initialize = FALSE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{metadata}{featMetaObj or data.table containing feature metadata. -Setting NULL will remove the object. Passing 'initialize' will reset the -object.} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{provenance}{provenance information to set} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning} -} -\value{ -giotto object -} -\description{ -Function to set feature metadata information into giotto object -} -\keyword{internal} diff --git a/man/set_giottoImage.Rd b/man/set_giottoImage.Rd deleted file mode 100644 index 48a9b7d0..00000000 --- a/man/set_giottoImage.Rd +++ /dev/null @@ -1,43 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_giottoImage} -\alias{set_giottoImage} -\title{Set giotto image object} -\usage{ -set_giottoImage( - gobject = NULL, - image = NULL, - image_type = NULL, - name = NULL, - verbose = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{image}{giotto image object to be attached without modification to the -giotto object} - -\item{image_type}{deprecated} - -\item{name}{name of giotto image object} - -\item{verbose}{be verbose} -} -\value{ -giotto object -} -\description{ -Directly attach a giotto image to giotto object -} -\details{ -\emph{\strong{Use with care!}} This function directly attaches -giotto image objects to the gobject without further modifications of -spatial positioning values within the image object that are generally -needed in order for them to plot in the correct location relative to the -other modalities of spatial data. \cr For the more general-purpose method -of attaching image objects, see \code{\link{addGiottoImage}} -} -\seealso{ -\code{\link{addGiottoImage}} -} diff --git a/man/set_giottoImage_MG.Rd b/man/set_giottoImage_MG.Rd deleted file mode 100644 index bf9cc1ad..00000000 --- a/man/set_giottoImage_MG.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_giottoImage_MG} -\alias{set_giottoImage_MG} -\title{Set \emph{magick}-based giotto \code{image}} -\usage{ -set_giottoImage_MG(gobject, image_object, name = NULL, verbose = NULL) -} -\arguments{ -\item{gobject}{giotto object} - -\item{image_object}{a giottoImage object} - -\item{name}{name to assign giottoImage} - -\item{verbose}{be verbose} -} -\value{ -giotto object -} -\description{ -Set a giottoImage for a giotto object with no additional -modifications -} -\keyword{internal} diff --git a/man/set_giottoLargeImage.Rd b/man/set_giottoLargeImage.Rd deleted file mode 100644 index b891509c..00000000 --- a/man/set_giottoLargeImage.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_giottoLargeImage} -\alias{set_giottoLargeImage} -\title{Set \emph{terra}-based giotto \code{largeImage}} -\usage{ -set_giottoLargeImage(gobject, largeImage_object, name = NULL, verbose = NULL) -} -\arguments{ -\item{gobject}{giotto object} - -\item{largeImage_object}{a giottoLargeImage object} - -\item{name}{name to assign giottoLargeImage} - -\item{verbose}{be verbose} -} -\value{ -giotto object -} -\description{ -Set a giottoLargeImage for a giotto object with no -additional modifications -} -\keyword{internal} diff --git a/man/set_multiomics.Rd b/man/set_multiomics.Rd index b82bd552..3d3c04f4 100644 --- a/man/set_multiomics.Rd +++ b/man/set_multiomics.Rd @@ -51,7 +51,6 @@ Other multiomics accessor functions: \code{\link{setMultiomics}()} Other functions to set data in giotto object: -\code{\link{get_feat_id}()}, \code{\link{setCellMetadata}()}, \code{\link{setDimReduction}()}, \code{\link{setExpression}()}, @@ -65,8 +64,7 @@ Other functions to set data in giotto object: \code{\link{setSpatialEnrichment}()}, \code{\link{setSpatialGrid}()}, \code{\link{setSpatialLocations}()}, -\code{\link{setSpatialNetwork}()}, -\code{\link{set_feat_id}()} +\code{\link{setSpatialNetwork}()} } \concept{functions to set data in giotto object} \concept{multiomics accessor functions} diff --git a/man/set_polygon_info.Rd b/man/set_polygon_info.Rd deleted file mode 100644 index 49b24027..00000000 --- a/man/set_polygon_info.Rd +++ /dev/null @@ -1,33 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_polygon_info} -\alias{set_polygon_info} -\title{Set polygon info} -\usage{ -set_polygon_info( - gobject, - gpolygon, - polygon_name = "cell", - verbose = TRUE, - initialize = FALSE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{gpolygon}{giottoPolygon object} - -\item{polygon_name}{name of polygons. Default -"cell" (only used when gpolygon is length of 1)} - -\item{verbose}{be verbose} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning} -} -\value{ -giotto object -} -\description{ -Set giotto polygon spatVector -} diff --git a/man/set_spatialGrid.Rd b/man/set_spatialGrid.Rd deleted file mode 100644 index 846ce155..00000000 --- a/man/set_spatialGrid.Rd +++ /dev/null @@ -1,39 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_spatialGrid} -\alias{set_spatialGrid} -\title{Set spatial grid} -\usage{ -set_spatialGrid( - gobject, - spatial_grid, - spat_unit = NULL, - feat_type = NULL, - name = NULL, - verbose = TRUE, - set_defaults = TRUE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spatial_grid}{spatial grid object} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{name}{name of spatial grid} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} -} -\value{ -giotto object -} -\description{ -Function to set a spatial grid -} diff --git a/man/set_spatialNetwork.Rd b/man/set_spatialNetwork.Rd deleted file mode 100644 index 99de860c..00000000 --- a/man/set_spatialNetwork.Rd +++ /dev/null @@ -1,43 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_spatialNetwork} -\alias{set_spatialNetwork} -\title{Set spatial network} -\usage{ -set_spatialNetwork( - gobject, - spatial_network, - spat_unit = NULL, - name = NULL, - provenance = NULL, - verbose = TRUE, - set_defaults = TRUE, - initialize = FALSE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spatial_network}{spatial network} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{name}{name of spatial network} - -\item{provenance}{provenance name} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning} -} -\value{ -giotto object -} -\description{ -Function to set a spatial network -} diff --git a/man/set_spatial_enrichment.Rd b/man/set_spatial_enrichment.Rd deleted file mode 100644 index d8f3a26e..00000000 --- a/man/set_spatial_enrichment.Rd +++ /dev/null @@ -1,46 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_spatial_enrichment} -\alias{set_spatial_enrichment} -\title{Set spatial enrichment} -\usage{ -set_spatial_enrichment( - gobject, - spatenrichment, - spat_unit = NULL, - feat_type = NULL, - enrichm_name = "enrichment", - provenance = NULL, - verbose = TRUE, - set_defaults = TRUE, - initialize = FALSE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spatenrichment}{spatial enrichment results} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{feat_type}{feature type (e.g. "rna", "dna", "protein")} - -\item{enrichm_name}{name of spatial enrichment results. Default "DWLS"} - -\item{provenance}{provenance information (optional)} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning} -} -\value{ -giotto object -} -\description{ -Function to set a spatial enrichment slot -} diff --git a/man/set_spatial_locations.Rd b/man/set_spatial_locations.Rd deleted file mode 100644 index 19924f73..00000000 --- a/man/set_spatial_locations.Rd +++ /dev/null @@ -1,55 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/slot_accessors.R -\name{set_spatial_locations} -\alias{set_spatial_locations} -\title{Set spatial locations} -\usage{ -set_spatial_locations( - gobject, - spatlocs, - spat_unit = NULL, - spat_loc_name = "raw", - provenance = NULL, - verbose = TRUE, - set_defaults = TRUE, - initialize = FALSE -) -} -\arguments{ -\item{gobject}{giotto object} - -\item{spatlocs}{spatial locations (accepts either \code{data.table} or -\code{spatLocsObj})} - -\item{spat_unit}{spatial unit (e.g. "cell")} - -\item{spat_loc_name}{name of spatial locations, default "raw"} - -\item{provenance}{provenance information (optional)} - -\item{verbose}{be verbose} - -\item{set_defaults}{set default spat_unit and feat_type. Change to FALSE -only when -expression and spat_info are not expected to exist.} - -\item{initialize}{(default = FALSE) whether to initialize the gobject before -returning} -} -\value{ -giotto object -} -\description{ -Function to set a spatial location slot -} -\details{ -If a \code{spatLocsObj} is provided to \code{spatlocs} param then -any attached name and spat_unit info will be used for input to this -function's \code{spat_loc_name} and \code{spat_unit}params, BUT will be -overridden by any alternative specific inputs to those params. \cr -ie: a \code{spatLocsObj} with spat_unit slot == 'cell' will be automatically -nested by spat_unit 'cell' when using \code{set_spatial_locations} as long as -param \code{spat_unit = NULL}. BUT if param \code{spat_unit = 'nucleus'} then -the \code{spatLocsObj} will be nested by spat_unit 'nucleus' instead and -its spat_unit slot will be changed to 'nucleus' -}