Merge pull request #1 from satijalab/master

Merge latest Seurat

.Rbuildignore

@@ -4,3 +4,4 @@
 .travis.yml
 appveyor.yml
 cran-comments.md
+travis_setup.sh

.travis.yml

@@ -1,29 +1,45 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
-language: R
+language: r
 sudo: required
-r_binary_packages:
-  - lars
-  - mixtools
-  - caret
-  - e1071
-  - ica
-  - fpc
-  - ape
-  - igraph
-  - dplyr
-  - irlba
-  - reshape2
-  - gdata
-  - compositions
-  - dtw
-  - plotly
-  - httr
-  - tidyr
-  - ranger
+cache: packages
+
+os:
+  - linux
+  - osx
+
+r: release
+
+env:
+  global:
+    - _R_CHECK_FORCE_SUGGESTS_=FALSE
+    - ASAN="-fsanitize=address -fno-omit-frame-pointer"
+    - LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
+    - HDF5_VERSION=1.8.17
+    - HDF5_RELEASE_URL="https://support.hdfgroup.org/ftp/HDF5/releases"
+
+before_install: 
+  - chmod +x travis_setup.sh
+  - ./travis_setup.sh
+
+addons:
+  apt:
+    packages:
+      - subversion
+      - autoconf
+      - build-essential
+      - libtool
+      - libmagick++-dev
+
 bioc_packages:
   - GenomeInfoDbData
   - DESeq2
   - MAST
+  - S4Vectors
+  - SummarizedExperiment
+  - SingleCellExperiment
+
+r_github_packages:
+  - mojaveazure/loomR
+
 warnings_are_errors: false
-dist: trusty

DESCRIPTION

@@ -1,53 +1,46 @@
 Package: Seurat
-Version: 2.3.0
-Date: 2018-03-22
+Version: 2.3.3
+Date: 2018-07-02
 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(
-  person(given = 'Rahul', family = 'Satija', email = '[email protected]', role = 'aut'),
-  person(given = 'Andrew', family = 'Butler', email = '[email protected]', role = 'aut'),
-  person(given = 'Paul', family = 'Hoffman', email = '[email protected]', role = c('aut', 'cre')),
+  person(given = 'Rahul', family = 'Satija', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
+  person(given = 'Andrew', family = 'Butler', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
+  person(given = 'Paul', family = 'Hoffman', email = '[email protected]', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),
   person(given = 'Jeff', family = 'Farrell', email = '[email protected]', role = 'ctb'),
-  person(given = 'Shiwei', family = 'Zheng', email = '[email protected]', role = 'ctb'),
-  person(given = 'Christoph', family = 'Hafemeister', email = '[email protected]', role = 'ctb'),
+  person(given = 'Shiwei', family = 'Zheng', email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0001-6682-6743')),
+  person(given = 'Christoph', family = 'Hafemeister', email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0001-6365-8254')),
   person(given = 'Patrick', family = 'Roelli', email = '[email protected]', role = 'ctb')
   )
 URL: http://www.satijalab.org/seurat, https://github.com/satijalab/seurat
 BugReports: https://github.com/satijalab/seurat/issues
+Additional_repositories: https://mojaveazure.github.io/loomR
 Depends:
-    R (>= 3.2.0),
+    R (>= 3.4.0),
     ggplot2,
     cowplot,
-    Matrix,
+    Matrix (>= 1.2.14),
 SystemRequirements: Java (>= 6)
 Imports:
     methods,
     ROCR,
-    stringr,
     mixtools,
     lars,
     ica,
     tsne,
     Rtsne,
     fpc,
     ape,
-    VGAM,
     pbapply,
     igraph,
-    FNN,
     RANN,
-    caret,
     dplyr,
     RColorBrewer,
     MASS,
     irlba,
     reshape2,
-    gridExtra,
     gplots,
-    gdata,
-    Rcpp,
-    tclust,
-    ranger,
+    Rcpp (>= 0.11.0),
     dtw,
     SDMTools,
     plotly,
@@ -61,14 +54,18 @@ Imports:
     fitdistrplus,
     png,
     doSNOW,
-    foreach
-LinkingTo: Rcpp, RcppEigen, RcppProgress
+    reticulate,
+    foreach,
+    hdf5r
+LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
 License: GPL-3 | file LICENSE
 LazyData: true
-Collate: 
+Collate:
     'RcppExports.R'
     'alignment.R'
     'seurat.R'
+    'conversion.R'
+    'as.R'
     'cluster_determination.R'
     'cluster_determination_internal.R'
     'cluster_validation.R'
@@ -99,7 +96,16 @@ Collate:
     'zfRenderSeurat.R'
 RoxygenNote: 6.0.1
 Suggests:
+    gdata,
+    VGAM,
+    tclust,
     testthat,
+    caret,
+    ranger,
+    loomR,
+    phateR,
+    S4Vectors,
     SummarizedExperiment,
+    SingleCellExperiment,
     MAST,
     DESeq2

NAMESPACE

@@ -1,5 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(Convert,SingleCellExperiment)
+S3method(Convert,anndata.base.AnnData)
+S3method(Convert,seurat)
+S3method(as.SingleCellExperiment,seurat)
+S3method(as.seurat,SingleCellExperiment)
 export(AddImputedScore)
 export(AddMetaData)
 export(AddModuleScore)
@@ -25,6 +30,7 @@ export(ClassifyCells)
 export(CollapseSpeciesExpressionMatrix)
 export(ColorTSNESplit)
 export(CombineIdent)
+export(Convert)
 export(CreateSeuratObject)
 export(CustomDistance)
 export(CustomPalette)
@@ -72,6 +78,7 @@ export(GetClusters)
 export(GetDimReduction)
 export(GetGeneLoadings)
 export(HTODemux)
+export(HTOHeatmap)
 export(HeatmapNode)
 export(HoverLocator)
 export(ICA)
@@ -132,9 +139,11 @@ export(ProjectDim)
 export(ProjectPCA)
 export(PurpleAndYellow)
 export(Read10X)
+export(Read10X_h5)
 export(RefinedMapping)
 export(RegressOut)
 export(RemoveFromTable)
+export(RenameCells)
 export(RenameIdent)
 export(ReorderIdent)
 export(RidgePlot)
@@ -143,7 +152,9 @@ export(RunDiffusion)
 export(RunICA)
 export(RunMultiCCA)
 export(RunPCA)
+export(RunPHATE)
 export(RunTSNE)
+export(RunUMAP)
 export(SampleUMI)
 export(SaveClusters)
 export(ScaleData)
@@ -179,6 +190,8 @@ export(addImputedScore)
 export(addMetaData)
 export(addSmoothedScore)
 export(add_samples)
+export(as.SingleCellExperiment)
+export(as.seurat)
 export(average.expression)
 export(average.pca)
 export(batch.gene)
@@ -268,21 +281,19 @@ import(diffusionMap)
 import(doSNOW)
 import(fpc)
 import(ggplot2)
-import(gridExtra)
 import(lars)
 import(metap)
-import(methods)
 import(parallel)
 import(pbapply)
-import(stringr)
-importFrom(FNN,get.knn)
 importFrom(Hmisc,cut2)
 importFrom(MASS,glm.nb)
 importFrom(MASS,kde2d)
 importFrom(MASS,negative.binomial)
 importFrom(MASS,theta.ml)
+importFrom(Matrix,colMeans)
 importFrom(Matrix,colSums)
 importFrom(Matrix,readMM)
+importFrom(Matrix,rowMeans)
 importFrom(Matrix,rowSums)
 importFrom(Matrix,sparseMatrix)
 importFrom(RANN,nn2)
@@ -291,14 +302,10 @@ importFrom(ROCR,performance)
 importFrom(ROCR,prediction)
 importFrom(Rcpp,evalCpp)
 importFrom(Rtsne,Rtsne)
-importFrom(VGAM,tobit)
-importFrom(VGAM,vgam)
 importFrom(ape,as.phylo)
 importFrom(ape,drop.tip)
 importFrom(ape,nodelabels)
 importFrom(ape,plot.phylo)
-importFrom(caret,train)
-importFrom(caret,trainControl)
 importFrom(cluster,clara)
 importFrom(cowplot,get_legend)
 importFrom(cowplot,plot_grid)
@@ -308,6 +315,7 @@ importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_each)
+importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
 importFrom(dplyr,summarize)
 importFrom(dplyr,summarize_each)
@@ -317,8 +325,6 @@ importFrom(dtw,dtw)
 importFrom(fitdistrplus,fitdist)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
-importFrom(gdata,drop.levels)
-importFrom(gdata,interleave)
 importFrom(ggplot2,annotation_raster)
 importFrom(ggridges,geom_density_ridges)
 importFrom(ggridges,theme_ridges)
@@ -341,6 +347,7 @@ importFrom(graphics,rect)
 importFrom(graphics,smoothScatter)
 importFrom(graphics,text)
 importFrom(graphics,title)
+importFrom(hdf5r,H5File)
 importFrom(ica,icafast)
 importFrom(ica,icaimax)
 importFrom(ica,icajade)
@@ -350,15 +357,32 @@ importFrom(igraph,graph.adjlist)
 importFrom(igraph,plot.igraph)
 importFrom(irlba,irlba)
 importFrom(lmtest,lrtest)
+importFrom(methods,"slot<-")
+importFrom(methods,.hasSlot)
+importFrom(methods,as)
+importFrom(methods,new)
+importFrom(methods,setClass)
+importFrom(methods,setMethod)
+importFrom(methods,signature)
+importFrom(methods,slot)
+importFrom(methods,slotNames)
 importFrom(mixtools,normalmixEM)
 importFrom(mixtools,plot.mixEM)
 importFrom(pbapply,pbapply)
 importFrom(pbapply,pblapply)
 importFrom(pbapply,pbsapply)
 importFrom(png,readPNG)
-importFrom(ranger,ranger)
 importFrom(reshape2,melt)
+importFrom(reticulate,dict)
+importFrom(reticulate,import)
+importFrom(reticulate,np_array)
+importFrom(reticulate,py_module_available)
+importFrom(reticulate,py_set_seed)
+importFrom(reticulate,py_to_r)
+importFrom(reticulate,r_to_py)
+importFrom(reticulate,tuple)
 importFrom(stats,anova)
+importFrom(stats,approx)
 importFrom(stats,as.dendrogram)
 importFrom(stats,as.dist)
 importFrom(stats,as.formula)
@@ -397,8 +421,9 @@ importFrom(stats,smooth.spline)
 importFrom(stats,t.test)
 importFrom(stats,var)
 importFrom(stats,wilcox.test)
-importFrom(tclust,tkmeans)
 importFrom(tidyr,gather)
+importFrom(tidyr,separate)
+importFrom(tidyr,unite)
 importFrom(tsne,tsne)
 importFrom(utils,file_test)
 importFrom(utils,globalVariables)

NEWS.md

@@ -2,6 +2,36 @@
 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/)
 
+## [2.3.3] - 2018-07-02
+### Added
+- New HTOHeatmap function
+- Support for custom PNG arguments for vector-friendly plotting
+- Fix for 'NA'-labeled cells disappearing with custom color scale
+
+### Changed
+- Replaced FNN with RANN
+- Removed unused compiler flags
+- Moved several lightly-used packages from 'imports' to 'suggests'
+
+
+## [2.3.2] - 2018-06-11
+### Added
+- RenameCells added for easy renaming of all cells
+- Read10X_h5 added to read in 10X formatted h5 files
+- SetAssayData ensures cell order is the same between assay objects and the Seurat object
+- Compatability updates for ggplot2 v2.3.0
+
+## [2.3.1] - 2018-05-03
+### Added
+- Support for [UMAP](https://github.com/lmcinnes/umap) dimensional reduction technique
+- New conversion functions for SingleCellExperiment and anndata
+
+### Changed
+- FetchData preserves cell order
+- Require Matrix 1.2-14 or higher
+- AddModuleScore no longer densifies sparse-matrices
+- Various visualization fixes and improvements
+- Default value for latent.vars in FindMarkers/FindAllMarkers changed to NULL.
 
 ## [2.3.0] - 2018-03-22
 ### Added