Add raster.dpi param for geom_scattermore (updated branch)

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 4.0.6
+Version: 4.0.6.9001
 Date: 2021-12-16
 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.

NEWS.md

@@ -1,3 +1,8 @@
+# Unreleased
+## Added
+- Add `raster.dpi` parameter to `DimPlot/FeaturePlot` to optionally rasterize individual points ([#5392](https://github.com/satijalab/seurat/pull/5392))
+
+
 # Seurat 4.0.6 (2021-12-16)
 ## Added
 

R/visualization.R

@@ -759,6 +759,8 @@ ColorDimSplit <- function(
 #' ggplot object. If \code{FALSE}, return a list of ggplot objects
 #' @param raster Convert points to raster format, default is \code{NULL} which
 #' automatically rasterizes if plotting more than 100,000 cells
+#' @param raster.dpi Pixel resolution for rasterized plots, passed to geom_scattermore().
+#' Default is c(512, 512).
 #'
 #' @return A \code{\link[patchwork]{patchwork}ed} ggplot object if
 #' \code{combine = TRUE}; otherwise, a list of ggplot objects
@@ -806,7 +808,8 @@ DimPlot <- function(
   na.value = 'grey50',
   ncol = NULL,
   combine = TRUE,
-  raster = NULL
+  raster = NULL,
+  raster.dpi = c(512, 512)
 ) {
   if (length(x = dims) != 2) {
     stop("'dims' must be a two-length vector")
@@ -853,7 +856,8 @@ DimPlot <- function(
         cols.highlight = cols.highlight,
         sizes.highlight = sizes.highlight,
         na.value = na.value,
-        raster = raster
+        raster = raster,
+        raster.dpi = raster.dpi
       )
       if (label) {
         plot <- LabelClusters(
@@ -995,7 +999,8 @@ FeaturePlot <- function(
   sort.cell = NULL,
   interactive = FALSE,
   combine = TRUE,
-  raster = NULL
+  raster = NULL,
+  raster.dpi = c(512, 512)
 ) {
   # TODO: deprecate fully on 3.2.0
   if (!is.null(x = sort.cell)) {
@@ -1257,7 +1262,8 @@ FeaturePlot <- function(
         cols = cols.use,
         shape.by = shape.by,
         label = FALSE,
-        raster = raster
+        raster = raster,
+        raster.dpi = raster.dpi
       ) +
         scale_x_continuous(limits = xlims) +
         scale_y_continuous(limits = ylims) +
@@ -1833,7 +1839,8 @@ CellScatter <- function(
   cols = NULL,
   pt.size = 1,
   smooth = FALSE,
-  raster = NULL
+  raster = NULL,
+  raster.dpi = c(512, 512)
 ) {
   features <- features %||% rownames(x = object)
   data <- FetchData(
@@ -1848,7 +1855,8 @@ CellScatter <- function(
     pt.size = pt.size,
     rows.highlight = highlight,
     smooth = smooth,
-    raster = raster
+    raster = raster,
+    raster.dpi = raster.dpi
   )
   return(plot)
 }
@@ -1880,6 +1888,8 @@ CellScatter <- function(
 #' @param raster Convert points to raster format, default is \code{NULL}
 #' which will automatically use raster if the number of points plotted is greater than
 #' 100,000
+#' @param raster.dpi Pixel resolution for rasterized plots, passed to geom_scattermore().
+#' Default is c(512, 512).
 #' @param jitter Jitter for easier visualization of crowded points
 #'
 #' @return A ggplot object
@@ -1913,6 +1923,7 @@ FeatureScatter <- function(
   slot = 'data',
   plot.cor = TRUE,
   raster = NULL,
+  raster.dpi = c(512, 512),
   jitter = TRUE
 ) {
   cells <- cells %||% colnames(x = object)
@@ -1955,6 +1966,7 @@ FeatureScatter <- function(
         span = span,
         plot.cor = plot.cor,
         raster = raster,
+        raster.dpi = raster.dpi,
         jitter = jitter
       )
     }
@@ -2000,7 +2012,8 @@ VariableFeaturePlot <- function(
   log = NULL,
   selection.method = NULL,
   assay = NULL,
-  raster = NULL
+  raster = NULL,
+  raster.dpi = c(512, 512)
 ) {
   if (length(x = cols) != 2) {
     stop("'cols' must be of length 2")
@@ -2034,7 +2047,8 @@ VariableFeaturePlot <- function(
     data = hvf.info,
     col.by = var.status,
     pt.size = pt.size,
-    raster = raster
+    raster = raster,
+    raster.dpi = raster.dpi
   )
   if (length(x = unique(x = var.status)) == 1) {
     switch(
@@ -6792,6 +6806,8 @@ globalVariables(names = '..density..', package = 'Seurat')
 #' @param raster Convert points to raster format, default is \code{NULL}
 #' which will automatically use raster if the number of points plotted is
 #' greater than 100,000
+#' @param raster.dpi the pixel resolution for rastered plots, passed to geom_scattermore().
+#' Default is c(512, 512)
 #' @param plot.cor ...
 #' @param jitter Jitter for easier visualization of crowded points
 #'
@@ -6819,6 +6835,7 @@ SingleCorPlot <- function(
   na.value = 'grey50',
   span = NULL,
   raster = NULL,
+  raster.dpi = NULL,
   plot.cor = TRUE,
   jitter = TRUE
 ) {
@@ -6828,6 +6845,10 @@ SingleCorPlot <- function(
             "\nTo disable this behavior set `raster=FALSE`")
   }
   raster <- raster %||% (nrow(x = data) > 1e5)
+  if (!is.null(x = raster.dpi)) {
+    if (!is.numeric(x = raster.dpi) || length(x = raster.dpi) != 2)
+      stop("'raster.dpi' must be a two-length numeric vector")
+  }
   orig.names <- colnames(x = data)
   names.plot <- colnames(x = data) <- gsub(
     pattern = '-',
@@ -6923,7 +6944,8 @@ SingleCorPlot <- function(
       plot <- plot + geom_scattermore(
         mapping = aes_string(color = 'colors'),
         position = position,
-        pointsize = pt.size
+        pointsize = pt.size,
+        pixels = raster.dpi
       )
     } else {
       plot <- plot + geom_point(
@@ -6934,7 +6956,7 @@ SingleCorPlot <- function(
     }
   } else {
     if (raster) {
-      plot <- plot + geom_scattermore(position = position, pointsize = pt.size)
+      plot <- plot + geom_scattermore(position = position, pointsize = pt.size, pixels = raster.dpi)
     } else {
       plot <- plot + geom_point(position = position, size = pt.size)
     }
@@ -6994,6 +7016,8 @@ SingleCorPlot <- function(
 #' @param raster Convert points to raster format, default is \code{NULL}
 #' which will automatically use raster if the number of points plotted is
 #' greater than 100,000
+#' @param raster.dpi the pixel resolution for rastered plots, passed to geom_scattermore().
+#' Default is c(512, 512)
 #'
 #' @return A ggplot2 object
 #'
@@ -7022,14 +7046,19 @@ SingleDimPlot <- function(
   cols.highlight = '#DE2D26',
   sizes.highlight = 1,
   na.value = 'grey50',
-  raster = NULL
+  raster = NULL,
+  raster.dpi = NULL
 ) {
   pt.size <- pt.size %||% AutoPointSize(data = data, raster = raster)
   if ((nrow(x = data) > 1e5) & !isFALSE(raster)){
     message("Rasterizing points since number of points exceeds 100,000.",
             "\nTo disable this behavior set `raster=FALSE`")
   }
   raster <- raster %||% (nrow(x = data) > 1e5)
+  if (!is.null(x = raster.dpi)) {
+    if (!is.numeric(x = raster.dpi) || length(x = raster.dpi) != 2)
+      stop("'raster.dpi' must be a two-length numeric vector")
+  }
   if (length(x = dims) != 2) {
     stop("'dims' must be a two-length vector")
   }
@@ -7113,7 +7142,8 @@ SingleDimPlot <- function(
         shape = shape.by,
         alpha = alpha.by
       ),
-      pointsize = pt.size
+      pointsize = pt.size,
+      pixels = raster.dpi
     )
   } else {
     plot + geom_point(