Merge branch 'develop' into fix/sce_conversion

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.2.9005
-Date: 2021-06-02
+Version: 4.0.2.9006
+Date: 2021-06-07
 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

@@ -7,6 +7,7 @@
 - Ensure proper reference.reduction is used in `MapQuery()`
 - Fix to `UpdateSymbolList()`, no longer searches aliases and exposes the `search.types` parameter in `GeneSymbolThesarus()` ([#4545](https://github.com/satijalab/seurat/issues/4545))
 - Transfer `scale.data` slot as well when converting with `as.SingleCellExperiment.Seurat()`
+- Enable `alpha` parameter for `SpatialDimPlot()`
 
 # Seurat 4.0.2 (2020-03-20)
 ## Added

R/visualization.R

@@ -2937,7 +2937,8 @@ ISpatialFeaturePlot <- function(
 #' themeing will not work when plotting multiple features/groupings
 #' @param pt.size.factor Scale the size of the spots.
 #' @param alpha Controls opacity of spots. Provide as a vector specifying the
-#' min and max
+#' min and max for SpatialFeaturePlot. For SpatialDimPlot, provide a single
+#' alpha value for each plot.
 #' @param stroke Control the width of the border around the spots
 #' @param interactive Launch an interactive SpatialDimPlot or SpatialFeaturePlot
 #' session, see \code{\link{ISpatialDimPlot}} or
@@ -3177,6 +3178,11 @@ SpatialPlot <- function(
         } else {
           NULL
         },
+        pt.alpha = if (!is.null(x = group.by)) {
+          alpha[j]
+        } else {
+          NULL
+        },
         geom = if (inherits(x = image.use, what = "STARmap")) {
           'poly'
         } else {
@@ -7484,6 +7490,7 @@ SingleRasterMap <- function(
 # By default, ggplot2 assigns colors
 # @param image.alpha Adjust the opacity of the background images. Set to 0 to
 # remove.
+# @param pt.alpha Adjust the opacity of the points if plotting a SpatialDimPlot
 # @param crop Crop the plot in to focus on points plotted. Set to FALSE to show
 # entire background image.
 # @param pt.size.factor Sets the size of the points relative to spot.radius
@@ -7510,6 +7517,7 @@ SingleSpatialPlot <- function(
   image,
   cols = NULL,
   image.alpha = 1,
+  pt.alpha = NULL,
   crop = TRUE,
   pt.size.factor = NULL,
   stroke = 0.25,
@@ -7550,14 +7558,27 @@ SingleSpatialPlot <- function(
   plot <- switch(
     EXPR = geom,
     'spatial' = {
-      plot + geom_spatial(
-        point.size.factor = pt.size.factor,
-        data = data,
-        image = image,
-        image.alpha = image.alpha,
-        crop = crop,
-        stroke = stroke
-      ) + coord_fixed() + theme(aspect.ratio = 1)
+      if (is.null(x = pt.alpha)) {
+        plot <- plot + geom_spatial(
+          point.size.factor = pt.size.factor,
+          data = data,
+          image = image,
+          image.alpha = image.alpha,
+          crop = crop,
+          stroke = stroke,
+        )
+      } else {
+        plot <- plot + geom_spatial(
+          point.size.factor = pt.size.factor,
+          data = data,
+          image = image,
+          image.alpha = image.alpha,
+          crop = crop,
+          stroke = stroke,
+          alpha = pt.alpha
+        )
+      }
+      plot + coord_fixed() + theme(aspect.ratio = 1)
     },
     'interactive' = {
       plot + geom_spatial_interactive(