Merge branch 'develop' into mix_fix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.1.9008
-Date: 2021-04-26
+Version: 4.0.1.9010
+Date: 2021-05-06
 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

@@ -16,6 +16,8 @@
 - Fix `DotPlot` to use `log1p` when `scale=False`
 ([#4298](https://github.com/satijalab/seurat/issues/4298))
 - Fix split and shuffled `DimPlot`
+- Disallow NULL or another length 0 vector for `ident.1` in `FindMarkers()`
+- Fix range shift when labeling clusters on a GeomSpatial plot
 
 # Seurat 4.0.1 (2020-03-17)
 ## Added

R/differential_expression.R

@@ -813,6 +813,9 @@ FindMarkers.Seurat <- function(
   if (!is.null(x = assay) && !is.null(x = reduction)) {
     stop("Please only specify either assay or reduction.")
   }
+  if (length(x = ident.1) == 0) {
+    stop("At least 1 ident must be specified in `ident.1`")
+  }
   # select which data to use
   if (is.null(x = reduction)) {
     assay <- assay %||% DefaultAssay(object = object)

R/visualization.R

@@ -4694,6 +4694,8 @@ LabelClusters <- function(
   }
   pb <- ggplot_build(plot = plot)
   if (geom == 'GeomSpatial') {
+    xrange.save <- layer_scales(plot = plot)$x$range$range
+    yrange.save <- layer_scales(plot = plot)$y$range$range
     data[, xynames["y"]] = max(data[, xynames["y"]]) - data[, xynames["y"]] + min(data[, xynames["y"]])
     if (!pb$plot$plot_env$crop) {
       y.transform <- c(0, nrow(x = pb$plot$plot_env$image)) - pb$layout$panel_params[[1]]$y.range
@@ -4771,6 +4773,10 @@ LabelClusters <- function(
       ...
     )
   }
+  # restore old axis ranges
+  if (geom == 'GeomSpatial') {
+    plot <- suppressMessages(expr = plot + coord_fixed(xlim = xrange.save, ylim = yrange.save))
+  }
   return(plot)
 }