Merge pull request #592 from satijalab/release/4.0.4

Prep for release of 4.0.4

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.3.9015
-Date: 2021-08-09
+Version: 4.0.4
+Date: 2021-08-19
 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

@@ -1,4 +1,4 @@
-## Unreleased
+## Seurat 4.0.4 (2020-08-19)
 ## Added
 - Add `reduction` parameter to `BuildClusterTree()` ([#4598](https://github.com/satijalab/seurat/issues/4598))
 - Add DensMAP option to `RunUMAP()` ([#4630](https://github.com/satijalab/seurat/pull/4630))
@@ -19,7 +19,7 @@
 - Fix issue in SingleCellExperiment conversion where the mainExp would not be set properly
 - Fix for default dispersion info displayed in `VariableFeaturePlot()`
 
-## Seurat 4.0.3 (2020-06-10)`
+## Seurat 4.0.3 (2020-06-10)
 ## Added
 - Add `jitter` parameter to `FeatureScatter()` 
 

R/dimensional_reduction.R

@@ -1514,7 +1514,7 @@ RunUMAP.Graph <- function(
       numeric_version(x = "0.5.0")) {
     umap.args <- c(umap.args, list(
       densmap = densmap,
-      densmap_kwds = densmap_kwds,
+      densmap_kwds = densmap.kwds,
       output_dens = FALSE
     ))
   }

cran-comments.md

@@ -1,11 +1,11 @@
-# Seurat v4.0.3
+# Seurat v4.0.4
 
 ## Test environments
-* local Ubuntu 20.04 install, R 4.0.5
+* local Ubuntu 20.04 install, R 4.1.0
 * Ubuntu 16.04.6 (on travis-ci), R 4.0.0, R devel
 * macOS 10.13.6 (on travis-ci), R 4.0.2
 * Windows Server 2012 R2 (on AppVeyor), R 4.1.0 Patched
-* win-builder (release, devel)
+* win-builder (oldrelease, release, devel)
 
 ## R CMD check results
 There were no ERRORs, WARNINGs, or NOTEs
@@ -14,6 +14,6 @@ There were no ERRORs, WARNINGs, or NOTEs
 
 There is one package that depends on Seurat: tidyseurat; this update does not impact its functionality
 
-There are seven packages that imports Seurat: CDSeq, DUBStepR, rPanglaoDB, scMappR, Signac, SignacX, and SoupX; this update does not impact their functionality
+There are eight packages that import Seurat: CDSeq, DUBStepR, PhitestR, rPanglaoDB, scMappR, Signac, SignacX, and SoupX; this update does not impact their functionality
 
-There are ten packages that suggest Seurat: BisqueRNA, ClustAssess, clustree, conos, DIscBIO, dyngen, harmony, rliger, Rmagic, VAM; this update does not impact their functionality.
+There are ten packages that suggest Seurat: BisqueRNA, ClustAssess, clustree, conos, DIscBIO, dyngen, harmony, rliger, Rmagic, and VAM; this update does not impact their functionality.

vignettes/spatial_vignette.Rmd

@@ -144,7 +144,9 @@ SpatialFeaturePlot(brain, features = c("Hpca", "Ttr"))
 library(ggplot2)
 plot <- SpatialFeaturePlot(brain, features = c("Ttr")) + 
   theme(legend.text = element_text(size = 0), legend.title = element_text(size = 20), legend.key.size = unit(1, "cm")) 
-ggsave(filename = "../output/images/spatial_vignette_ttr.jpg", height = 7, width = 12, plot = plot, quality = 50)
+jpeg(filename = "../output/images/spatial_vignette_ttr.jpg", height = 700, width = 1200, quality = 50)
+print(plot)
+dev.off()
 ```
 
 The default parameters in Seurat emphasize the visualization of molecular data. However, you can also adjust the size of the spots (and their transparency) to improve the visualization of the histology image, by changing the following parameters: