From 19d635f0571424c926dcf79ac22998db449f9328 Mon Sep 17 00:00:00 2001 From: Andrew Date: Mon, 9 Aug 2021 12:07:50 -0400 Subject: [PATCH 1/5] update DESCRIPTION and NEWS --- DESCRIPTION | 4 ++-- NEWS.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2fdbc7b79..2d4a461ba 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Seurat -Version: 4.0.3.9015 -Date: 2021-08-09 +Version: 4.0.4 +Date: 2021-08-10 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) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 63b6758c0..959669d02 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -## Unreleased +## Seurat 4.0.4 (2020-08-10) ## 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()` From 8de9a839976bf3b869aeb7d6069b7904ef7b0e76 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Mon, 9 Aug 2021 12:56:51 -0400 Subject: [PATCH 2/5] Fix to RunUMAP.Graph --- R/dimensional_reduction.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 0ece584eb..c6e61a789 100644 --- a/R/dimensional_reduction.R +++ b/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 )) } From 6c21601b525c8604ff0cd3b0b0e587bedba29e57 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Mon, 9 Aug 2021 13:00:55 -0400 Subject: [PATCH 3/5] Update CRAN comments --- cran-comments.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 2bff06026..b3ecc32a8 100644 --- a/cran-comments.md +++ b/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. From 235113ab5c33a6660ba8a6885eed8242fe24a6f7 Mon Sep 17 00:00:00 2001 From: Andrew Butler Date: Tue, 10 Aug 2021 16:43:17 -0400 Subject: [PATCH 4/5] switch saving method --- vignettes/spatial_vignette.Rmd | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/vignettes/spatial_vignette.Rmd b/vignettes/spatial_vignette.Rmd index 0f09b211b..cad2ef62e 100644 --- a/vignettes/spatial_vignette.Rmd +++ b/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: From 3c1dbf64090e01cdc8a680a938cc0250725febc8 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Thu, 19 Aug 2021 16:15:19 -0400 Subject: [PATCH 5/5] Update dates --- DESCRIPTION | 2 +- NEWS.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2d4a461ba..fae9265ce 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Seurat Version: 4.0.4 -Date: 2021-08-10 +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) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 959669d02..16332f784 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -## Seurat 4.0.4 (2020-08-10) +## 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))