Merge pull request satijalab#261 from satijalab/release/3.1.4

Prep for CRAN release of 3.1.4

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.1.3.9005
-Date: 2020-02-20
+Version: 3.1.4
+Date: 2020-02-21
 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>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
 Authors@R: c(

NEWS.md

@@ -2,7 +2,12 @@
 All notable changes to Seurat will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 
-## [3.1.3] = 2020-02-07
+## [3.1.4] - 2020-02-20
+### Changes 
+- Fixes to `DoHeatmap` to remain compatible with ggplot2 v3.3
+- Adoption of `patchwork` framework to replace `CombinePlots`
+
+## [3.1.3] - 2020-02-07
 ### Added
 - New system agnostic `Which` function to address problems with FItSNE on Windows
 

R/visualization.R

@@ -747,6 +747,7 @@ DimPlot <- function(
   data <- as.data.frame(x = data)
   dims <- paste0(Key(object = object[[reduction]]), dims)
   object[['ident']] <- Idents(object = object)
+  orig.groups <- group.by
   group.by <- group.by %||% 'ident'
   data[, group.by] <- object[[group.by]][cells, , drop = FALSE]
   for (group in group.by) {
@@ -800,11 +801,11 @@ DimPlot <- function(
       return(plot)
     }
   )
-  if( !is.null(x = split.by) && length(x = group.by) > 1) {
+  if (!is.null(x = split.by)) {
     ncol <- 1
   }
   if (combine) {
-    plots <- wrap_plots(plots, ncol = ncol)
+    plots <- wrap_plots(plots, ncol = orig.groups %iff% ncol)
   }
   return(plots)
 }
@@ -1241,7 +1242,6 @@ FeaturePlot <- function(
                 yes = levels(x = data$split)[ii],
                 no = ''
               )),
-              limits = ylims,
               expand = c(0, 0)
             ) +
             labs(
@@ -1327,21 +1327,16 @@ FeaturePlot <- function(
             theme(plot.title = element_text(hjust = 0.5))
           idx <- idx + 1
         }
-        idx <- 1
-        if (length(x = features) == 1) {
-          for (i in 1:length(x = plots)) {
-            plots[[i]] <- plots[[i]] + ggtitle(levels(x = data$split)[[idx]]) + theme(plot.title = element_text(hjust = 0.5))
-            idx <- idx + 1
-          }
-        }
-        plots <- plots[c(do.call(
-          what = rbind,
-          args = split(x = 1:length(x = plots), f = ceiling(x = seq_along(along.with = 1:length(x = plots))/length(x = features)))
-        ))]
-        plots <- wrap_plots(plots, ncol = nsplits)
+        ncol <- nsplits
+        nrow <- 1
       } else {
-        plots <- wrap_plots(plots, ncol = ncol, nrow = split.by %iff% length(x = levels(x = data$split)))
+        nrow <- split.by %iff% length(x = levels(x = data$split))
       }
+      plots <- plots[c(do.call(
+        what = rbind,
+        args = split(x = 1:length(x = plots), f = ceiling(x = seq_along(along.with = 1:length(x = plots)) / length(x = features)))
+      ))]
+      plots <- wrap_plots(plots, ncol = ncol, nrow = nrow)
       if (!is.null(x = legend) && legend == 'none') {
         plots <- plots & NoLegend()
       }
@@ -3749,6 +3744,9 @@ ExIPlot <- function(
   }
   if (combine) {
     plots <- wrap_plots(plots, ncol = ncol)
+    if (length(x = features) > 1) {
+      plots <- plots & NoLegend()
+    }
   }
   return(plots)
 }

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 v3.1.3
+# Seurat v3.1.4
 
 
 Seurat is an R toolkit for single cell genomics, developed and maintained by the Satija Lab at NYGC.

cran-comments.md

@@ -1,7 +1,8 @@
-# Seurat v3.1.3
+# Seurat v3.1.4
 
 ## Test environments
 * local Ubuntu 16.04.6 and 18.04.2 installs, R 3.6.1
+* local Windows 10 install, R 3.5.3
 * Ubuntu 16.04.6 (on travis-ci), R 3.6.1
 * macOS 10.13.3 (on travis-ci), R 3.6.1
 * Windows Server 2012 R2 (on AppVeyor), R 3.6.1 Patched
@@ -13,30 +14,23 @@ There were no ERRORs or WARNINGs
 There were 3 NOTEs:
 
 * checking CRAN incoming feasibility ... NOTE
-    Maintainer: ‘Paul Hoffman <[email protected]>’
+  Maintainer: ‘Paul Hoffman <[email protected]>’
 
-    New submission
+  Suggests or Enhances not in mainstream repositories:
+    loomR, SDMTools
+  Availability using Additional_repositories specification:
+    loomR      yes   https://mojaveazure.github.io/loomR
+    SDMTools    no   ?
 
-    Package was archived on CRAN
-
-    CRAN repository db overrides:
-        X-CRAN-Comment: Archived on 2020-02-07 as check issues were not
-            corrected in time.
-
-    Suggests or Enhances not in mainstream repositories:
-        loomR
-    Availability using Additional_repositories specification:
-        loomR   yes   https://mojaveazure.github.io/loomR
-
-  This is a patch for an archived package Seurat. We were slow in fixing the errors and would like to get Seurat back on CRAN. In addition. the package we suggest, loomR, is currently under development and not yet available on CRAN. This package is not required for core functionality of Seurat.
+  One of the packages we suggest, loomR, is currently under development and not yet available on CRAN. This package is not required for core functionality of Seurat. The other package, SDMTools is also not required for core functionality. We are working to replace the function that calls SDMTools with a new function using non-orphaned packages
 
 * checking package dependencies ... NOTE
   Package suggested but not available for checking: 'loomR'
-  
+
   Suggests orphaned package: ‘SDMTools’
 
   loomR is a suggested package hosted on a custom repository and maintained by us (both the package and repository).
-  
+
   SDMTools is not required for any essential functionality. We are working to replace the function that calls SDMTools with a new function using non-orphaned packages.
 
 * checking Rd cross-references ... NOTE
@@ -48,4 +42,4 @@ There were 3 NOTEs:
 
 There is one pacakge that imports Seurat: multicross; this update does not impact its functionality
 
-There are five packages that suggest Seurat: BisqueRNA, clustree, diem, iCellR, and Rmagic; this update does not impact their functionality.
+There are three packages that suggest Seurat: BisqueRNA, clustree, and Rmagic; this update does not impact their functionality.