Merge pull request #8180 from samuel-marsh/dimplot_stroke

Add stroke.size parameter DimPlot

Author: dcollins15

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 5.1.0.9014
+Version: 5.1.0.9015
 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.
 Authors@R: c(

NEWS.md

@@ -1,6 +1,7 @@
 # Unreleased
 
 ## Changes
+- Added `stroke.size` parameter to `DimPlot` ([#8180](https://github.com/satijalab/seurat/pull/8180))
 - Updated `RunLeiden` to use the `leidenbase` package instead of `leiden`; deprecated the `method` parameter for `RunLeiden` and `FindClusters`; updated `RunLeiden` to reset `random.seed` to 1 if the value is 0 or less ([#6792](https://github.com/satijalab/seurat/pull/6792))
 - Updated `RunUMAP` to support `umap-learn` version >= 0.5.0 ([#9559](https://github.com/satijalab/seurat/pull/9559))
 - Surfaced more fine-grained control over what parts of a Xenium experiment are loaded in `LoadXenium`

R/preprocessing.R

@@ -852,7 +852,7 @@ LoadCurioSeeker <- function(data.dir, assay = "Spatial") {
 #' @export
 #' @concept preprocessing
 #'
-#' @references \url{https://www.biorxiv.org/content/10.1101/387241v1}
+#' @references \url{https://doi.org/10.1038/s41592-019-0433-8}
 #'
 #' @examples
 #' \dontrun{

R/visualization.R

@@ -815,6 +815,7 @@ ColorDimSplit <- function(
 #' geom_label)
 #' @param alpha Alpha value for plotting (default is 1)
 #' @param repel Repel labels
+#' @param stroke.size Adjust stroke (outline) size of points
 #' @param cells.highlight A list of character or numeric vectors of cells to
 #' highlight. If only one group of cells desired, can simply
 #' pass a vector instead of a list. If set, colors selected cells to the color(s)
@@ -875,6 +876,7 @@ DimPlot <- function(
   label.box = FALSE,
   repel = FALSE,
   alpha = 1,
+  stroke.size = NULL,
   cells.highlight = NULL,
   cols.highlight = '#DE2D26',
   sizes.highlight = 1,
@@ -941,6 +943,7 @@ DimPlot <- function(
         shape.by = shape.by,
         order = order,
         alpha = alpha,
+        stroke.size = stroke.size,
         label = FALSE,
         cells.highlight = cells.highlight,
         cols.highlight = cols.highlight,
@@ -8182,6 +8185,7 @@ SingleCorPlot <- function(
 #' allowing for both different colors and different shapes on cells.
 #' @param alpha Alpha value for plotting (default is 1)
 #' @param alpha.by Mapping variable for the point alpha value
+#' @param stroke.size Adjust stroke (outline) size of points
 #' @param order Specify the order of plotting for the idents. This can be
 #' useful for crowded plots if points of interest are being buried. Provide
 #' either a full list of valid idents or a subset to be plotted last (on top).
@@ -8224,6 +8228,7 @@ SingleDimPlot <- function(
   shape.by = NULL,
   alpha = 1,
   alpha.by = NULL,
+  stroke.size = NULL,
   order = NULL,
   label = FALSE,
   repel = FALSE,
@@ -8242,6 +8247,10 @@ SingleDimPlot <- function(
   raster <- raster %||% (nrow(x = data) > 1e5)
   pt.size <- pt.size %||% AutoPointSize(data = data, raster = raster)
 
+  if (is.null(x = stroke.size)) {
+    stroke.size <- 0.600075815011372
+  }
+
   if (!is.null(x = cells.highlight) && pt.size != AutoPointSize(data = data, raster = raster) && sizes.highlight != pt.size && isTRUE(x = raster)) {
     warning("When `raster = TRUE` highlighted and non-highlighted cells must be the same size. Plot will use the value provided to 'sizes.highlight'.")
   }
@@ -8352,7 +8361,8 @@ SingleDimPlot <- function(
         alpha = alpha.by
       ),
       size = pt.size,
-      alpha = alpha
+      alpha = alpha,
+      stroke = stroke.size
     )
   }
   plot <- plot +