Update updateCellChat to rename meta$slices as meta$samples

R/CellChat_class.R

@@ -155,14 +155,18 @@ createCellChat <- function(object, meta = NULL, group.by = NULL,
  .error_if_no_Seurat()
  print("Create a CellChat object from a Seurat object")
  if (is.null(assay)) {
- assay = DefaultAssay(object)
+ assay = Seurat::DefaultAssay(object)
  if (assay == "integrated") {
- warning("The data in the `integrated` assay is not suitable for CellChat analysis! Please use the `RNA` or `SCT` assay! ")
+ warning("The data in the `integrated` assay is not suitable for CellChat analysis! Please use the `RNA`, `SCT` or `Spatial` assay! ")
  }
  cat(paste0("The `data` slot in the default assay is used. The default assay is ", assay),'\n')
  }
-
- data <- Seurat::GetAssayData(object, assay = assay, slot = "data") # normalized data matrix
+ if (packageVersion("Seurat") < "5.0.0") {
+ # data <- Seurat::GetAssayData(object, assay = assay, slot = "data") # normalized data matrix
+ data <- object[[assay]]@data
+ } else {
+ data <- object[[assay]]$data
+ }
  if (min(data) < 0) {
  stop("The data matrix contains negative values. Please ensure the normalized data matrix is used.")
  }
@@ -176,8 +180,7 @@ createCellChat <- function(object, meta = NULL, group.by = NULL,
  }
  if (datatype %in% c("spatial")) {
  if (is.null(coordinates)) {
- coordinates <- GetTissueCoordinates(object, scale = NULL, cols = c("imagerow", "imagecol"))
- # spatial.factors <- object@images[["slice1"]]@spatial.factors
+ coordinates <- Seurat::GetTissueCoordinates(object, scale = NULL, cols = c("imagerow", "imagecol"))
  }
  }
 
@@ -244,26 +247,23 @@ createCellChat <- function(object, meta = NULL, group.by = NULL,
  meta = meta)
 
  if (!is.null(meta) & nrow(meta) > 0) {
+ if (!("samples" %in% colnames(meta))) {
+ warning("The 'meta' data does not have a column named `samples`. We now add this column and all cells are assumed to belong to `sample1`!")
+ meta$samples <- "sample1"
+ meta$samples <- factor(meta$samples)
+ object@meta <- meta
+ } else if (is.factor(meta$samples) == FALSE) {
+ warning("The 'meta$samples' is not a factor. We now force it as a factor!")
+ meta$samples <- factor(meta$samples)
+ object@meta <- meta
+ }
+
  cat("Set cell identities for the new CellChat object", '\n')
  if (!(group.by %in% colnames(meta))) {
  stop("The 'group.by' is not a column name in the `meta`, which will be used for cell grouping.")
  }
  object <- setIdent(object, ident.use = group.by) # set "labels" as default cell identity
  cat("The cell groups used for CellChat analysis are ", toString(levels(object@idents)), '\n')
-
- if (datatype %in% c("spatial")) {
- if (!("slices" %in% colnames(meta))) {
- warning("The 'meta' data does not have a column named `slices` for spatial transcriptomics data analysis.
- We now add this column and all cells are assigned as `slice1`!")
- meta$slices <- "slice1"
- meta$slices <- factor(meta$slices)
- object@meta <- meta
- } else if (is.factor(meta$slices) == FALSE) {
- warning("The 'meta$slices' is not a factor. We now force it as a factor!")
- meta$slices <- factor(meta$slices)
- object@meta <- meta
- }
- }
  }
 
  object@options$mode <- "single"
@@ -416,6 +416,8 @@ mergeCellChat <- function(object.list, add.names = NULL, merge.data = FALSE, cel
 #'
 #' version 2.1.1: `images$scale.factors` is changed to `images$spatial.factors` for spatial transcriptomics data analysis.
 #'
+#' version 2.1.2: the column `slices` in `object@meta` is renamed as `samples` in order to identify consistent signaling across samples for cell-cell communication analysis.
+#'
 #' @param object CellChat object
 #'
 #' @return a updated CellChat object
@@ -451,17 +453,19 @@ updateCellChat <- function(object) {
  images = object@images
  }
  meta = object@meta
+ if ("slices" %in% colnames(meta)) {
+ meta$samples <- meta$slices
+ meta$slices = NULL
+ }
+ if (!("samples" %in% colnames(meta))) {
+ warning("The 'meta' data does not have a column named `samples`. We now add this column and all cells are assumed to belong to `sample1`!")
+ meta$samples <- "sample1"
+ meta$samples <- factor(meta$samples)
+ } else if (is.factor(meta$samples) == FALSE) {
+ warning("The 'meta$samples' is not a factor. We now force it as a factor!")
+ meta$samples <- factor(meta$samples)
+ }
  if (object@options$datatype %in% c("spatial")) {
- if (!("slices" %in% colnames(meta))) {
- warning("The 'meta' data does not have a column named `slices` for spatial transcriptomics data analysis.
- We now add this column and all cells are assigned as `slice1`!")
- meta$slices <- "slice1"
- meta$slices <- factor(meta$slices)
- } else if (is.factor(meta$slices) == FALSE) {
- warning("The 'meta$slices' is not a factor. We now force it as a factor!")
- meta$slices <- factor(meta$slices)
- }
-
  if ("scale.factors" %in% names(object@images)) {
  images$spatial.factors <- as.data.frame(images$scale.factors)
  images$scale.factors <- NULL