Merge branch 'CRAN'

Author: Paul Hoffman

.gitignore

@@ -6,3 +6,4 @@ src/*.o
 src/*.so
 .DS_Store
 *.pdf
+*.Rproj

.travis.yml

@@ -21,5 +21,9 @@ r_binary_packages:
   - httr
   - tidyr
   - ranger
+bioc_packages:
+  - GenomeInfoDbData
+  - DESeq2
+  - MAST
 warnings_are_errors: false
 dist: trusty

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 2.0.1
-Date: 2017-08-18
+Version: 2.1.0
+Date: 2017-10-11
 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(
@@ -36,7 +36,6 @@ Imports:
     igraph,
     FNN,
     caret,
-    e1071,
     dplyr,
     RColorBrewer,
     MASS,
@@ -48,9 +47,7 @@ Imports:
     Rcpp,
     tclust,
     ranger,
-    compositions,
     NMF,
-    NMOF,
     dtw,
     SDMTools,
     plotly,
@@ -61,7 +58,7 @@ Imports:
 LinkingTo: Rcpp, RcppEigen, RcppProgress
 License: GPL-3 | file LICENSE
 LazyData: true
-Collate:
+Collate: 
     'RcppExports.R'
     'seurat.R'
     'cluster_determination.R'
@@ -94,4 +91,7 @@ Collate:
     'zfRenderSeurat.R'
 RoxygenNote: 6.0.1
 Suggests:
-    testthat
+    testthat,
+    SummarizedExperiment,
+    MAST,
+    DESeq2

NAMESPACE

@@ -20,12 +20,14 @@ export(CaseMatch)
 export(CellCycleScoring)
 export(CellPlot)
 export(ClassifyCells)
+export(CollapseSpeciesExpressionMatrix)
 export(ColorTSNESplit)
 export(CreateSeuratObject)
 export(CustomDistance)
 export(CustomPalette)
 export(DBClustDimension)
 export(DBclust_dimension)
+export(DESeq2DETest)
 export(DMEmbed)
 export(DMPlot)
 export(DarkTheme)
@@ -84,6 +86,7 @@ export(KMeansHeatmap)
 export(Kclust_dimension)
 export(LogNormalize)
 export(LogVMR)
+export(MASTDETest)
 export(MakeSparse)
 export(MarkerTest)
 export(MatrixRowShuffle)
@@ -161,6 +164,7 @@ export(VizICA)
 export(VizPCA)
 export(VlnPlot)
 export(WhichCells)
+export(WilcoxDETest)
 export(addImputedScore)
 export(addMetaData)
 export(addSmoothedScore)
@@ -363,6 +367,7 @@ importFrom(stats,prop.test)
 importFrom(stats,qqplot)
 importFrom(stats,quantile)
 importFrom(stats,qunif)
+importFrom(stats,relevel)
 importFrom(stats,reorder)
 importFrom(stats,residuals)
 importFrom(stats,rnorm)
@@ -371,10 +376,13 @@ importFrom(stats,sd)
 importFrom(stats,smooth.spline)
 importFrom(stats,t.test)
 importFrom(stats,var)
+importFrom(stats,wilcox.test)
 importFrom(tclust,tkmeans)
 importFrom(tidyr,gather)
 importFrom(tsne,tsne)
 importFrom(utils,globalVariables)
+importFrom(utils,installed.packages)
+importFrom(utils,menu)
 importFrom(utils,packageVersion)
 importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)

NEWS.md

@@ -2,6 +2,14 @@
 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/)
 
+## [2.1.0] - 2017-10-12
+### Added
+- Support for using MAST and DESeq2 packages for differential expression testing in FindMarkers
+- Support for multi-modal single-cell data via @assay slot
+
+### Changed
+- Default DE test changed to Wilcoxon rank sum test
+
 ## [2.0.1] - 2017-08-18
 ### Added
  - Now available on CRAN

R/cluster_determination.R

@@ -100,8 +100,8 @@ FindClusters <- function(
   }
   if ((
     missing(x = genes.use) && missing(x = dims.use) && missing(x = k.param) &&
-    missing(x = k.scale) && missing(x = prune.SNN) && snn.built
-  ) || reuse.SNN) {
+    missing(x = k.scale) && missing(x = prune.SNN)  && missing(x = distance.matrix) 
+    && snn.built) || reuse.SNN) {
     save.SNN <- TRUE
     if (reuse.SNN && !snn.built) {
       stop("No SNN stored to reuse.")
@@ -116,6 +116,9 @@ FindClusters <- function(
   } else {
     # if any SNN building parameters are provided or it hasn't been built, build
     # a new SNN
+    if(!is.null(distance.matrix)) {
+      force.recalc <- TRUE
+    }
     object <- BuildSNN(
       object = object,
       genes.use = genes.use,
@@ -135,10 +138,12 @@ FindClusters <- function(
     parameters.to.store$resolution <- r
     if (CalcInfoExists(object, paste0("FindClusters.res.", r)) & force.recalc != TRUE){
       parameters.to.store$object <- NULL
+      parameters.to.store$print.output <- NULL
       old.parameters <- GetAllCalcParam(object = object,
                                         calculation = paste0("FindClusters.res.", r))
       old.parameters$time <- NULL
-      if(all(suppressWarnings(unlist(lapply(X = 1:length(old.parameters), function(x) old.parameters[[x]] == parameters.to.store[[x]]))))){
+      old.parameters$print.output <- NULL
+      if(all(all.equal(old.parameters, parameters.to.store) == TRUE)){
         warning(paste0("Clustering parameters for resolution ", r, " exactly match those of already computed. \n  To force recalculation, set force.recalc to TRUE."))
         object <- SetAllIdent(object, paste0("res.", r))
         next

R/deprecated_functions.R

@@ -605,6 +605,57 @@ RegressOut <- function(...) {
   stop()
 }
 
+PCAFast <- function(...) {
+  .Deprecated("PCA", package= "Seurat")
+  PCA(...)
+}
+
+writ.table <- function(...) {
+  .Deprecated(
+    new = 'write.table',
+    package = 'Seurat',
+    msg = "'writ.table' no longer exists, use 'write.table' instead"
+  )
+}
+
+jackRandom <- function(...) {
+  .Deprecated(new = 'JackRandom', package = 'Seurat')
+  JackRandom(...)
+}
+
+MeanVarPlot <- function(...) {
+  .Deprecated(new = 'FindVariableGenes', package = 'Seurat')
+  FindVariableGenes(...)
+}
+
+HeatmapNode <- function(...) {
+  .Deprecated(new = 'NodeHeatmap', package = 'Seurat')
+  NodeHeatmap(...)
+}
+
+myPalette <- function(...) {
+  .Deprecated(new = 'CustomPalette', package = 'Seurat')
+  CustomPalette(...)
+}
+
+minusr <- function(...) {
+  .Deprecated(
+    new = 'SubsetRow',
+    package = 'Seurat',
+    msg = "Use SubsetRow with 'invert = TRUE' instead"
+  )
+  SubsetRow(..., invert = TRUE)
+}
+
+minusc <- function(...) {
+  .Deprecated(
+    new = 'SubsetColumn',
+    package = 'Seurat',
+    msg = "Use SubsetColumn with 'invert = TRUE' instead"
+  )
+  SubsetColumn(..., invert = TRUE)
+}
+
 VizClassification <- function(...) {
   .Deprecated(
     package = 'Seurat',