Rename the slot data.project as data.smooth in the CellChat object

R/CellChat_class.R

@@ -18,7 +18,7 @@ setClassUnion(name = 'AnyFactor', members = c("factor", "list"))
 #' @slot data normalized data matrix for CellChat analysis (Genes should be in rows and cells in columns)
 #' @slot data.signaling a subset of normalized matrix only containing signaling genes
 #' @slot data.scale scaled data matrix
-#' @slot data.project projected data
+#' @slot data.smooth smoothed data
 #' @slot images a list of information of spatial transcriptomics data
 #' @slot net a three-dimensional array P (K×K×N), where K is the number of cell groups and N is the number of ligand-receptor pairs. Each row of P indicates the communication probability originating from the sender cell group to other cell groups.
 #' @slot netP a three-dimensional array representing cel-cell communication networks on a signaling pathway level
@@ -39,7 +39,7 @@ CellChat <- methods::setClass("CellChat",
  data = 'AnyMatrix',
  data.signaling = "AnyMatrix",
  data.scale = "matrix",
- data.project = "AnyMatrix",
+ data.smooth = "AnyMatrix",
  images = "list",
  net = "list",
  netP = "list",
@@ -143,7 +143,7 @@ createCellChat <- function(object, meta = NULL, group.by = NULL,
  assay = NULL, do.sparse = T) {
  datatype <- match.arg(datatype)
  # data matrix as input
- if (inherits(x = object, what = c("matrix", "Matrix", "dgCMatrix"))) {
+ if (inherits(x = object, what = c("matrix", "Matrix", "dgCMatrix", "dgRMatrix","CsparseMatrix"))) {
  print("Create a CellChat object from a data matrix")
  data <- object
  if (is.null(group.by)) {
@@ -208,6 +208,9 @@ createCellChat <- function(object, meta = NULL, group.by = NULL,
  }
 
  if (!inherits(x = data, what = c("dgCMatrix")) & do.sparse) {
+ if (inherits(x = data, what = c("dgRMatrix"))) {
+ data <- as(data, "CsparseMatrix")
+ }
  data <- as(data, "dgCMatrix")
  }
 
@@ -251,12 +254,12 @@ createCellChat <- function(object, meta = NULL, group.by = NULL,
 
  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`!")
+ 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`! \n")
  meta$samples <- "sample1"
  meta$samples <- factor(meta$samples)
  object@meta <- meta
  } else if (is.factor(meta$samples) == FALSE) {
- warning("The 'meta$samples' is not a factor. We now force it as a factor!")
+ warning("The 'meta$samples' is not a factor. We now force it as a factor! \n")
  meta$samples <- factor(meta$samples)
  object@meta <- meta
  }
@@ -421,6 +424,8 @@ mergeCellChat <- function(object.list, add.names = NULL, merge.data = FALSE, cel
 #'
 #' 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.
 #'
+#' version 2.1.3: the slot `[email protected]` is renamed as `[email protected]`.
+#'
 #' @param object CellChat object
 #'
 #' @return a updated CellChat object
@@ -474,13 +479,18 @@ updateCellChat <- function(object) {
  images$scale.factors <- NULL
  }
  }
+ if ("data.smooth" %in% methods::slotNames(object) == FALSE) {
+ data.smooth <- object@data.project
+ } else {
+ data.smooth <- object@data.smooth
+ }
  object.new <- methods::new(
  Class = "CellChat",
  data.raw = object@data.raw,
  data = object@data,
  data.signaling = object@data.signaling,
  data.scale = object@data.scale,
- data.project = object@data.project,
+ data.smooth = data.smooth,
  images = images,
  net = net,
  netP = object@netP,
@@ -769,10 +779,10 @@ subsetCellChat <- function(object, cells.use = NULL, idents.use = NULL, group.by
  } else {
  data.subset <- matrix(0, nrow = 0, ncol = 0)
  }
- if (nrow(object@data.project) > 0) {
- data.project.subset <- object@data.project[, cells.use.index]
+ if (nrow(object@data.smooth) > 0) {
+ data.smooth.subset <- object@data.smooth[, cells.use.index]
  } else {
- data.project.subset <- matrix(0, nrow = 0, ncol = 0)
+ data.smooth.subset <- matrix(0, nrow = 0, ncol = 0)
  }
  data.signaling.subset <- object@data.signaling[, cells.use.index]
 
@@ -936,7 +946,7 @@ subsetCellChat <- function(object, cells.use = NULL, idents.use = NULL, group.by
  Class = "CellChat",
  data = data.subset,
  data.signaling = data.signaling.subset,
- data.project = data.project.subset,
+ data.smooth = data.smooth.subset,
  images = images.subset,
  net = net.subset,
  netP = netP.subset,