Merge branch 'develop' into fix/heatmap

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 4.0.3.9010
+Version: 4.0.3.9011
 Date: 2021-07-16
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

NAMESPACE

@@ -264,6 +264,7 @@ export(Read10X)
 export(Read10X_Image)
 export(Read10X_h5)
 export(ReadMtx)
+export(ReadParseBio)
 export(ReadSTARsolo)
 export(ReadSlideSeq)
 export(Reductions)

NEWS.md

@@ -5,6 +5,7 @@
 - Add `image` parameter to `Load10X_Spatial()` and `image.name` parameter to `Read10X_Image()` ([#4641](https://github.com/satijalab/seurat/pull/4641))
 - Add `ReadSTARsolo()` function to read output from STARsolo
 - Add `densify` parameter to `FindMarkers()`
+- Add `ReadParsebio()` function to read output from Parse Biosciences
 
 ## Changes
 - Warn and continue rather than erroring if not all features are available in `FindSpatiallyVariableFeatures()` ([#4611](https://github.com/satijalab/seurat/issues/4611))

R/convenience.R

@@ -172,16 +172,41 @@ SpecificDimPlot <- function(object, ...) {
   )
 }
 
+#' Read output from Parse Biosciences
+#'
+#' @param data.dir Directory containing the data files
+#' @param ... Extra parameters passed to \code{\link{ReadMtx}}
+#' @concept convenience
+#' @export
+#'
+ReadParseBio <- function(data.dir, ...) {
+  mtx <- file.path(data.dir, "DGE.mtx")
+  cells <- file.path(data.dir, "cell_metadata.csv")
+  features <- file.path(data.dir, "genes.csv")
+  return(ReadMtx(
+    mtx = mtx,
+    cells = cells,
+    features = features,
+    cell.column = 1,
+    feature.column = 2,
+    cell.sep = ",",
+    feature.sep = ",",
+    skip.cell = 1,
+    skip.feature = 1,
+    mtx.transpose = TRUE
+  ))
+}
+
 #' Read output from STARsolo
 #'
 #' @param data.dir Directory containing the data files
-#' @param ... Extra parameters passed to \code{ReadMtx}
+#' @param ... Extra parameters passed to \code{\link{ReadMtx}}
 #'
 #' @rdname ReadSTARsolo
 #' @concept convenience
 #' @export
 #'
-ReadSTARsolo <- function(data.dir, ... ){
+ReadSTARsolo <- function(data.dir, ... ) {
   mtx <- file.path(data.dir, "matrix.mtx")
   cells <- file.path(data.dir, "barcodes.tsv")
   features <- file.path(data.dir, "features.tsv")

R/preprocessing.R

@@ -1045,8 +1045,11 @@ Read10X_Image <- function(image.dir, image.name = "tissue_lowres_image.png", fil
 #' @param features Name or remote URL of the features/genes file
 #' @param cell.column Specify which column of cells file to use for cell names; default is 1
 #' @param feature.column Specify which column of features files to use for feature/gene names; default is 2
+#' @param cell.sep Specify the delimiter in the cell name file
+#' @param feature.sep Specify the delimiter in the feature name file
 #' @param skip.cell Number of lines to skip in the cells file before beginning to read cell names
 #' @param skip.feature Number of lines to skip in the features file before beginning to gene names
+#' @param mtx.transpose Transpose the matrix after reading in
 #' @param unique.features Make feature names unique (default TRUE)
 #' @param strip.suffix Remove trailing "-1" if present in all cell barcodes.
 #'
@@ -1085,8 +1088,11 @@ ReadMtx <- function(
   features,
   cell.column = 1,
   feature.column = 2,
+  cell.sep = "\t",
+  feature.sep = "\t",
   skip.cell = 0,
   skip.feature = 0,
+  mtx.transpose = FALSE,
   unique.features = TRUE,
   strip.suffix = FALSE
 ) {
@@ -1118,14 +1124,14 @@ ReadMtx <- function(
   cell.barcodes <- read.table(
     file = all.files[['barcode list']],
     header = FALSE,
-    sep = '\t',
+    sep = cell.sep,
     row.names = NULL,
     skip = skip.cell
   )
   feature.names <- read.table(
     file = all.files[['feature list']],
     header = FALSE,
-    sep = '\t',
+    sep = feature.sep,
     row.names = NULL,
     skip = skip.feature
   )
@@ -1196,6 +1202,9 @@ ReadMtx <- function(
     feature.names <- make.unique(names = feature.names)
   }
   data <- readMM(file = all.files[['expression matrix']])
+  if (mtx.transpose) {
+    data <- t(x = data)
+  }
   if (length(x = cell.names) != ncol(x = data)) {
     stop(
       "Matrix has ",