Merge pull request #808 from satijalab/release/4.4.0

Release/4.4.0
satijalab · Sep 27, 2023 · d9f09de · d9f09de
2 parents f20de9d + 820f29d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.3.0.9013
-Date: 2023-07-21
+Version: 4.4.0
+Date: 2023-09-26
 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(
@@ -58,6 +58,7 @@ Imports:
     plotly (>= 4.9.0),
     png,
     progressr,
+    purrr,
     RANN,
     RColorBrewer,
     Rcpp (>= 1.0.7),
@@ -67,9 +68,9 @@ Imports:
     ROCR,
     Rtsne,
     scales,
-    scattermore (>= 0.7),
-    sctransform (>= 0.3.5),
-    SeuratObject (>= 4.1.3),
+    scattermore (>= 1.2),
+    sctransform (>= 0.4.0),
+    SeuratObject (>= 4.1.4),
     shiny,
     spatstat.explore,
     spatstat.geom,

diff --git a/NAMESPACE b/NAMESPACE
@@ -674,6 +674,7 @@ importFrom(plotly,plot_ly)
 importFrom(plotly,raster2uri)
 importFrom(png,readPNG)
 importFrom(progressr,progressor)
+importFrom(purrr,imap)
 importFrom(reticulate,import)
 importFrom(reticulate,py_module_available)
 importFrom(reticulate,py_set_seed)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# Unreleased
+# Seurat 4.4.0 (2023-09-27)
 
 ## Added
 - Added parallelization support with speed improvements for `PrepSCTFindMarkers` 
@@ -7,11 +7,12 @@
 ## Changes
 - Fix bug in `as.Seurat.SingleCellExperiment()` ([#6692](https://github.com/satijalab/seurat/issues/6692))
 - Support for Visium probe information introduced in Spaceranger 2.1 ([#7141](https://github.com/satijalab/seurat/pull/7141))
-- Add `LoadCurioSeeker` to load sequencing-based spatial datasets generated using the Curio Seeker ([#744](https://github.com/satijalab/seurat-private/pull/744))
-- Fix fold change calculation for assays ([#739](https://github.com/satijalab/seurat-private/pull/739))
+- Add `LoadCurioSeeker` to load sequencing-based spatial datasets generated using the Curio Seeker 
+- Fix fold change calculation for assays ([#7095](https://github.com/satijalab/seurat/issues/7095))
 - Fix `pt.size` bug when rasterization is set to true ([#7379](https://github.com/satijalab/seurat/issues/7379)) 
 - Fix `FoldChange` and `FindMarkers` to support all normalization approaches ([#7115](https://github.com/satijalab/seurat/pull/7115),[#7110](https://github.com/satijalab/seurat/issues/7110),[#7095](https://github.com/satijalab/seurat/issues/7095),[#6976](https://github.com/satijalab/seurat/issues/6976),[#6654](https://github.com/satijalab/seurat/issues/6654),[#6701](https://github.com/satijalab/seurat/issues/6701),[#6773](https://github.com/satijalab/seurat/issues/6773), [#7107](https://github.com/satijalab/seurat/issues/7107))
 - Fix for handling newer ParseBio formats in `ReadParseBio` ([#7565](https://github.com/satijalab/seurat/pull/7565))
+- Fix for handling rasterization by default ([#7842](https://github.com/satijalab/seurat/pull/7842))
 
 # Seurat 4.3.0 (2022-11-18)
 

diff --git a/R/preprocessing.R b/R/preprocessing.R
@@ -488,6 +488,7 @@ GetResidual <- function(
 #' @importFrom png readPNG
 #' @importFrom grid rasterGrob
 #' @importFrom jsonlite fromJSON
+#' @importFrom purrr imap
 #'
 #' @export
 #' @concept preprocessing
@@ -519,7 +520,7 @@ Load10X_Spatial <- function(
 
   if (to.upper) {
     data <- imap(data, ~{
-      rownames(.x) <- toupper(rownames(.x))
+      rownames(.x) <- toupper(x = rownames(.x))
       .x
     })
   }

diff --git a/R/visualization.R b/R/visualization.R
@@ -4009,7 +4009,7 @@ SpatialPlot <- function(
       }
 
       # Get feature max for individual feature
-      if (!(is.null(x = keep.scale)) && keep.scale == "feature" && class(x = data[, features[j]]) != "factor") {
+      if (!(is.null(x = keep.scale)) && keep.scale == "feature" && !inherits(x = data[, features[j]], what = "factor") ) {
         max.feature.value <- max(data[, features[j]])
       }
 
@@ -4085,7 +4085,7 @@ SpatialPlot <- function(
       }
 
       # Plot multiple images depending on keep.scale
-      if (!(is.null(x = keep.scale)) && class(x = data[, features[j]]) != "factor") {
+      if (!(is.null(x = keep.scale)) && !inherits(x = data[, features[j]], "factor")) {
         plot <- suppressMessages(plot & scale_fill_gradientn(colors = SpatialColors(n = 100), limits = c(NA, max.feature.value)))
       }
 
@@ -4885,7 +4885,7 @@ AutoPointSize <- function(data, raster = NULL) {
 #' hexadecimal codes
 #' @param threshold Intensity threshold for light/dark cutoff; intensities
 #' greater than \code{theshold} yield \code{dark}, others yield \code{light}
-#' @param w3c Use \href{http://www.w3.org/TR/WCAG20/}{W3C} formula for calculating
+#' @param w3c Use \href{https://www.w3.org/TR/WCAG20/}{W3C} formula for calculating
 #' background text color; ignores \code{threshold}
 #' @param dark Color for dark text
 #' @param light Color for light text
@@ -7802,7 +7802,7 @@ globalVariables(names = '..density..', package = 'Seurat')
 #' @param cols An optional vector of colors to use
 #' @param pt.size Point size for the plot
 #' @param smooth Make a smoothed scatter plot
-#' @param rows.highight A vector of rows to highlight (like cells.highlight in
+#' @param rows.highlight A vector of rows to highlight (like cells.highlight in
 #' \code{\link{SingleDimPlot}})
 #' @param legend.title Optional legend title
 #' @param raster Convert points to raster format, default is \code{NULL}
@@ -7842,7 +7842,7 @@ SingleCorPlot <- function(
   jitter = TRUE
 ) {
   pt.size <- pt.size %||% AutoPointSize(data = data, raster = raster)
-  if ((nrow(x = data) > 1e5) & !isFALSE(raster)){
+  if ((nrow(x = data) > 1e5) & !is.null(x = raster)){
     message("Rasterizing points since number of points exceeds 100,000.",
             "\nTo disable this behavior set `raster=FALSE`")
   }
@@ -8051,7 +8051,7 @@ SingleDimPlot <- function(
   raster = NULL,
   raster.dpi = NULL
 ) {
-  if ((nrow(x = data) > 1e5) & !isFALSE(raster)){
+  if ((nrow(x = data) > 1e5) & is.null(x = raster)){
     message("Rasterizing points since number of points exceeds 100,000.",
             "\nTo disable this behavior set `raster=FALSE`")
   }
@@ -8245,7 +8245,7 @@ SingleExIPlot <- function(
   if (PackageCheck('ggrastr', error = FALSE)) {
     # Set rasterization to true if ggrastr is installed and
     # number of points exceeds 100,000
-    if ((nrow(x = data) > 1e5) & !isFALSE(raster)){
+    if ((nrow(x = data) > 1e5) & is.null(x = raster)){
       message("Rasterizing points since number of points exceeds 100,000.",
               "\nTo disable this behavior set `raster=FALSE`")
       # change raster to TRUE

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![CRAN Version](https://www.r-pkg.org/badges/version/Seurat)](https://cran.r-project.org/package=Seurat)
 [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Seurat)](https://cran.r-project.org/package=Seurat)
 
-# Seurat v4.3.0
+# Seurat v4.4.0
 
 Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,30 +1,16 @@
-# Seurat v4.2.1
+# Seurat v4.4.0
 
 ## Test environments
-* local Ubuntu 20.04 install, R 4.1.3
+* local Ubuntu 20.04 install, R 4.3.1
 * win-builder (release, devel)
 
 ## R CMD check results
-There were no ERRORs or WARNINGs
-
-There was one NOTE:
-
-* checking CRAN incoming feasibility ... NOTE
-Maintainer: 'Paul Hoffman <seurat@nygenome.org>'
-
-Found the following (possibly) invalid URLs:
-  URL: https://www.science.org/doi/abs/10.1126/science.aad0501
-    From: man/cc.genes.Rd
-          man/cc.genes.updated.2019.Rd
-    Status: 503
-    Message: Service Unavailable
-
-This URL is valid and the service still exists. When navigating to the URL either via the documentation or directly, you are taken to the correct article
+There were no ERRORs or WARNINGs.
 
 ## Downstream dependencies
 
 There no packages that depend on Seurat
 
-There are sixteen packages that import Seurat: CAMML, CIDER, DR.SC, DUBStepR, maple, Platypus, rPanglaoDB, scDiffCom, scMappR, SCRIP, scRNAstat, Signac, SignacX, SoupX, spruce, and tidyseurat; this update does not impact their functionality
+There are forty-five packages that import Seurat: AnanseSeurat, APL, bbknnR, benchdamic, CAMML, CIDER, COTAN, CSCDRNA, Dino, DR.SC, DWLS, ggsector, gsdensity, infercnv, IRISFGM, mixhvg, Nebulosa, pipeComp, PRECAST, ProFAST, rPanglaoDB, scAnnotate, scBFA, scBubbletree, scCB2, scDataviz, scDiffCom, scFeatures, scGate, scMappR, scperturbR, scpoisson, SCRIP, scRNAseqApp, scRNAstat, scTreeViz, SignacX, singleCellTK, SoupX, Spaniel, SPECK, speckle, SpotClean, stJoincount, and STREAK; this update does not impact their functionality
 
-There are twelve packages that suggest Seurat: BisqueRNA, CIARA, ClustAssess, clustree, conos, DIscBIO, dyngen, harmony, rliger, Rmagic, treefit, and VAM; this update does not impact their functionality.
+There are fifty-one packages that suggest Seurat: ASURAT, BayesSpace, BisqueRNA, Canek, cellpypes, CIARA, ClustAssess, clustifyr, clustifyrdatahub, clustree, combiroc, conos, countland, CRMetrics, decoupleR, DIscBIO, dittoSeq, dorothea, dyngen, EasyCellType, EpiMix, escape, fcoex, FEAST, fgsea, GeomxTools, grandR, harmony, M3Drop, MOFA2, monocle, muscData, progeny, RESET, rliger, SCORPIUS, SCpubr, scRepertoire, scTensor, Signac, SimBenchData, SimBu, spatialHeatmap, SPOTlight, TAPseq, TCGAbiolinks, tidybulk, treefit, tricycle, UCell, and VAM; this update does not impact their functionality.
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,31 +1,33 @@
 citHeader("To cite Seurat in publications, please use:")
 
-citEntry(entry = "article",
-  author = personList(as.person("Yuhan Hao"),
-                      as.person("Stephanie Hao"),
-                      as.person("Erica Andersen-Nissen"),
-                      as.person("William M. Mauck III"),
-                      as.person("Shiwei Zheng"),
-                      as.person("Andrew Butler"),
-                      as.person("Maddie J. Lee"),
-                      as.person("Aaron J. Wilk"),
-                      as.person("Charlotte Darby"),
-                      as.person("Michael Zagar"),
-                      as.person("Paul Hoffman"),
-                      as.person("Marlon Stoeckius"),
-                      as.person("Efthymia Papalexi"),
-                      as.person("Eleni P. Mimitou"),
-                      as.person("Jaison Jain"),
-                      as.person("Avi Srivastava"),
-                      as.person("Tim Stuart"),
-                      as.person("Lamar B. Fleming"),
-                      as.person("Bertrand Yeung"),
-                      as.person("Angela J. Rogers"),
-                      as.person("Juliana M. McElrath"),
-                      as.person("Catherine A. Blish"),
-                      as.person("Raphael Gottardo"),
-                      as.person("Peter Smibert"),
-                      as.person("Rahul Satija")),
+bibentry(bibtype = "article",
+  author = c(
+  as.person("Yuhan Hao"),
+  as.person("Stephanie Hao"),
+  as.person("Erica Andersen-Nissen"),
+  as.person("William M. Mauck III"),
+  as.person("Shiwei Zheng"),
+  as.person("Andrew Butler"),
+  as.person("Maddie J. Lee"),
+  as.person("Aaron J. Wilk"),
+  as.person("Charlotte Darby"),
+  as.person("Michael Zagar"),
+  as.person("Paul Hoffman"),
+  as.person("Marlon Stoeckius"),
+  as.person("Efthymia Papalexi"),
+  as.person("Eleni P. Mimitou"),
+  as.person("Jaison Jain"),
+  as.person("Avi Srivastava"),
+  as.person("Tim Stuart"),
+  as.person("Lamar B. Fleming"),
+  as.person("Bertrand Yeung"),
+  as.person("Angela J. Rogers"),
+  as.person("Juliana M. McElrath"),
+  as.person("Catherine A. Blish"),
+  as.person("Raphael Gottardo"),
+  as.person("Peter Smibert"),
+  as.person("Rahul Satija")
+  ),
   title = "Integrated analysis of multimodal single-cell data",
   journal = "Cell",
   year = "2021",
@@ -34,17 +36,19 @@ citEntry(entry = "article",
   textVersion = "Hao and Hao et al. Integrated analysis of multimodal single-cell data. Cell (2021) [Seurat V4]"
 )
 
-citEntry(entry = "article",
-  author = personList(as.person("Tim Stuart"),
-                      as.person("Andrew Butler"),
-                      as.person("Paul Hoffman"),
-                      as.person("Christoph Hafemeister"),
-                      as.person("Efthymia Papalexi"),
-                      as.person("William M Mauck III"),
-                      as.person("Yuhan Hao"),
-                      as.person("Marlon Stoeckius"),
-                      as.person("Peter Smibert"),
-                      as.person("Rahul Satija")),
+bibentry(bibtype = "article",
+  author = c(
+  as.person("Tim Stuart"),
+  as.person("Andrew Butler"),
+  as.person("Paul Hoffman"),
+  as.person("Christoph Hafemeister"),
+  as.person("Efthymia Papalexi"),
+  as.person("William M Mauck III"),
+  as.person("Yuhan Hao"),
+  as.person("Marlon Stoeckius"),
+  as.person("Peter Smibert"),
+  as.person("Rahul Satija")
+  ),
   title = "Comprehensive Integration of Single-Cell Data",
   journal = "Cell",
   year = "2019",
@@ -55,12 +59,14 @@ citEntry(entry = "article",
   textVersion = "Stuart and Butler et al. Comprehensive Integration of Single-Cell Data. Cell (2019) [Seurat V3]"
 )
 
-citEntry(entry = "article",
-  author = personList(as.person("Andrew Butler"),
-                      as.person("Paul Hoffman"),
-                      as.person("Peter Smibert"),
-                      as.person("Efthymia Papalexi"),
-                      as.person("Rahul Satija")),
+bibentry(bibtype = "article",
+  author = c(
+  as.person("Andrew Butler"),
+  as.person("Paul Hoffman"),
+  as.person("Peter Smibert"),
+  as.person("Efthymia Papalexi"),
+  as.person("Rahul Satija")
+  ),
   title = "Integrating single-cell transcriptomic data across different conditions, technologies, and species",
   journal = "Nature Biotechnology",
   year = "2018",
@@ -71,12 +77,14 @@ citEntry(entry = "article",
   textVersion = "Butler et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol (2018) [Seurat V2]"
 )
 
-citEntry(entry = "article",
-  author = personList(as.person("Rahul Satija"),
-                      as.person("Jeffrey A Farrell"),
-                      as.person("David Gennert"),
-                      as.person("Alexander F Schier"),
-                      as.person("Aviv Regev")),
+bibentry(bibtype = "article",
+  author = c(
+  as.person("Rahul Satija"),
+  as.person("Jeffrey A Farrell"),
+  as.person("David Gennert"),
+  as.person("Alexander F Schier"),
+  as.person("Aviv Regev")
+  ),
   title = "Spatial reconstruction of single-cell gene expression data",
   journal = "Nature Biotechnology",
   year = "2015",

diff --git a/man/BGTextColor.Rd b/man/BGTextColor.Rd
diff --git a/man/SingleCorPlot.Rd b/man/SingleCorPlot.Rd