Preserve row and column names when creating an Assay

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SeuratObject
 Type: Package
 Title: Data Structures for Single Cell Data
-Version: 4.0.0.9001
-Date: 2021-01-19
+Version: 4.0.0.9002
+Date: 2021-02-12
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),

R/assay.R

@@ -67,6 +67,7 @@ Assay <- setClass(
 #' new object with a lower cutoff.
 #' @param min.features Include cells where at least this many features are
 #' detected.
+#' @param ... Arguments passed to \code{\link{as.sparse}}
 #'
 #' @return A \code{\link{Assay}} object
 #'
@@ -91,7 +92,8 @@ CreateAssayObject <- function(
   counts,
   data,
   min.cells = 0,
-  min.features = 0
+  min.features = 0,
+  ...
 ) {
   if (missing(x = counts) && missing(x = data)) {
     stop("Must provide either 'counts' or 'data'")
@@ -125,7 +127,7 @@ CreateAssayObject <- function(
       stop("No feature names (rownames) names present in the input matrix")
     }
     if (!inherits(x = counts, what = 'dgCMatrix')) {
-      counts <- as(object = as.matrix(x = counts), Class = 'dgCMatrix')
+      counts <- as.sparse(x = counts, ...)
     }
     # Filter based on min.features
     if (min.features > 0) {

R/seurat.R

@@ -909,6 +909,10 @@ Command.Seurat <- function(object, command = NULL, value = NULL, ...) {
   return(params[[value]])
 }
 
+#' @param row.names When \code{counts} is a \code{data.frame} or
+#' \code{data.frame}-derived object: an optional vector of feature names to be
+#' used
+#'
 #' @rdname CreateSeuratObject
 #' @method CreateSeuratObject default
 #' @export
@@ -922,6 +926,7 @@ CreateSeuratObject.default <- function(
   meta.data = NULL,
   min.cells = 0,
   min.features = 0,
+  row.names = NULL,
   ...
 ) {
   if (!is.null(x = meta.data)) {
@@ -932,7 +937,8 @@ CreateSeuratObject.default <- function(
   assay.data <- CreateAssayObject(
     counts = counts,
     min.cells = min.cells,
-    min.features = min.features
+    min.features = min.features,
+    row.names = row.names
   )
   if (!is.null(x = meta.data)) {
     common.cells <- intersect(

R/utils.R

@@ -232,12 +232,21 @@ RowMergeSparseMatrices <- function(mat1, mat2) {
 # Methods for Seurat-defined generics
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
+#' @param row.names \code{NULL} or a character vector giving the row names for
+#' the data; missing values are not allowed
+#'
 #' @rdname as.sparse
 #' @export
 #' @method as.sparse data.frame
 #'
-as.sparse.data.frame <- function(x, ...) {
+as.sparse.data.frame <- function(x, row.names = NULL, ...) {
   CheckDots(...)
+  dnames <- list(row.names %||% rownames(x = x), colnames(x = x))
+  if (length(x = dnames[[1]]) != nrow(x = x)) {
+    stop("Differing numbers of rownames and rows", call. = FALSE)
+  }
+  x <- as.data.frame(x = x)
+  dimnames(x = x) <- dnames
   return(as.sparse(x = as.matrix(x = x)))
 }