Merge pull request #2002 from satijalab/develop

Seurat v3.1.0

.Rbuildignore

@@ -6,3 +6,4 @@
 appveyor.yml
 cran-comments.md
 travis_setup.sh
+CODE_OF_CONDUCT.md

.travis.yml

@@ -8,7 +8,14 @@ os:
   - linux
   - osx
 
-r: release
+r:
+  - release
+  - devel
+
+matrix:
+  exclude:
+    - r: devel
+      os: osx
 
 env:
   global:
@@ -18,7 +25,7 @@ env:
     - HDF5_VERSION=1.8.17
     - HDF5_RELEASE_URL="https://support.hdfgroup.org/ftp/HDF5/releases"
 
-before_install: 
+before_install:
   - chmod +x travis_setup.sh
   - ./travis_setup.sh
 

CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at rsatija@nygenome.org. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.0.2
-Date: 2019-06-14
+Version: 3.1.0
+Date: 2019-08-20
 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(
@@ -11,7 +11,8 @@ Authors@R: c(
   person(given = 'Jeff', family = 'Farrell', email = 'jfarrell@g.harvard.edu', role = 'ctb'),
   person(given = 'Shiwei', family = 'Zheng', email = 'szheng@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-6682-6743')),
   person(given = 'Christoph', family = 'Hafemeister', email = 'chafemeister@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-6365-8254')),
-  person(given = 'Patrick', family = 'Roelli', email = 'proelli@nygenome.org', role = 'ctb')
+  person(given = 'Patrick', family = 'Roelli', email = 'proelli@nygenome.org', role = 'ctb'),
+  person(given = "Yuhan", family = "Hao", email = 'yhao@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-1810-0822'))
   )
 URL: http://www.satijalab.org/seurat, https://github.com/satijalab/seurat
 BugReports: https://github.com/satijalab/seurat/issues
@@ -36,16 +37,18 @@ Imports:
     igraph,
     irlba,
     KernSmooth,
+    leiden (>= 0.3.1),
     lmtest,
     MASS,
-    Matrix (>= 1.2.14),
+    Matrix (>= 1.2-14),
     metap,
     pbapply,
     plotly,
     png,
     RANN,
     RColorBrewer,
     Rcpp,
+    RcppAnnoy,
     reticulate,
     rlang,
     ROCR,
@@ -57,7 +60,8 @@ Imports:
     stats,
     tools,
     tsne,
-    utils
+    utils,
+    uwot
 LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
 License: GPL-3 | file LICENSE
 LazyData: true

NAMESPACE

@@ -161,6 +161,7 @@ export("VariableFeatures<-")
 export(ALRAChooseKPlot)
 export(AddMetaData)
 export(AddModuleScore)
+export(Assays)
 export(AugmentPlot)
 export(AverageExpression)
 export(BarcodeInflectionsPlot)
@@ -174,7 +175,9 @@ export(CellCycleScoring)
 export(CellScatter)
 export(CellSelector)
 export(Cells)
+export(CollapseEmbeddingOutliers)
 export(CollapseSpeciesExpressionMatrix)
+export(ColorDimSplit)
 export(CombinePlots)
 export(Command)
 export(CreateAssayObject)
@@ -249,6 +252,7 @@ export(PercentageFeatureSet)
 export(PlotClusterTree)
 export(PolyDimPlot)
 export(PolyFeaturePlot)
+export(PrepSCTIntegration)
 export(Project)
 export(ProjectDim)
 export(PurpleAndYellow)
@@ -257,6 +261,7 @@ export(Read10X_h5)
 export(ReadAlevin)
 export(ReadAlevinCsv)
 export(ReadH5AD)
+export(Reductions)
 export(RelativeCounts)
 export(RenameCells)
 export(RenameIdents)
@@ -320,7 +325,6 @@ import(Matrix)
 importClassesFrom(Matrix,dgCMatrix)
 importFrom(KernSmooth,bkde)
 importFrom(MASS,glm.nb)
-importFrom(MASS,kde2d)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,as.matrix)
 importFrom(Matrix,colMeans)
@@ -334,6 +338,10 @@ importFrom(RColorBrewer,brewer.pal.info)
 importFrom(ROCR,performance)
 importFrom(ROCR,prediction)
 importFrom(Rcpp,evalCpp)
+importFrom(RcppAnnoy,AnnoyAngular)
+importFrom(RcppAnnoy,AnnoyEuclidean)
+importFrom(RcppAnnoy,AnnoyHamming)
+importFrom(RcppAnnoy,AnnoyManhattan)
 importFrom(Rtsne,Rtsne)
 importFrom(SDMTools,pnt.in.poly)
 importFrom(ape,as.phylo)
@@ -435,8 +443,11 @@ importFrom(ica,icaimax)
 importFrom(ica,icajade)
 importFrom(igraph,E)
 importFrom(igraph,graph.adjacency)
+importFrom(igraph,graph_from_adj_list)
+importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(igraph,plot.igraph)
 importFrom(irlba,irlba)
+importFrom(leiden,leiden)
 importFrom(lmtest,lrtest)
 importFrom(metap,minimump)
 importFrom(methods,"slot<-")
@@ -492,7 +503,6 @@ importFrom(stats,na.omit)
 importFrom(stats,p.adjust)
 importFrom(stats,pchisq)
 importFrom(stats,pnbinom)
-importFrom(stats,pnorm)
 importFrom(stats,poisson)
 importFrom(stats,prcomp)
 importFrom(stats,prop.test)
@@ -513,14 +523,18 @@ importFrom(tsne,tsne)
 importFrom(utils,.DollarNames)
 importFrom(utils,argsAnywhere)
 importFrom(utils,browseURL)
+importFrom(utils,capture.output)
 importFrom(utils,file_test)
-importFrom(utils,getAnywhere)
 importFrom(utils,globalVariables)
+importFrom(utils,isS3method)
+importFrom(utils,isS3stdGeneric)
+importFrom(utils,methods)
 importFrom(utils,packageVersion)
 importFrom(utils,read.csv)
 importFrom(utils,read.delim)
 importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
 importFrom(utils,write.table)
+importFrom(uwot,umap)
 useDynLib(Seurat)

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/)
 
+## [3.1.0] - 2019-08-20
+### Added
+- New `PrepSCTIntegrati
+- on` function to facilitate integration after `SCTransform`
+- Reference-based integration with the `reference` parameter in `FindIntegrationAnchors`
+- Reciprocal PCA as a `reduction` option in `FindIntegrationAnchors`
+- New `CollapseEmbeddingOutliers` function
+- Enable `FindTransferAnchors` after `SCTransform`
+- Added back `ColorDimSplit` functionality
+- Include a code of conduct
+- Added uwot support as new default UMAP method
+- Added `CheckDots` to catch unused parameters and suggest updated names
+- `Reductions` and `Assays` assays functions to list stored DimReducs and Assays
+
+### Changed
+- Fix regex in `LogSeuratCommand`
+- Check for NAs in feature names in `Read10X`
+- Prevent dimnames for counts/data/scale.data matrices from being arrays
+- Updates `ReadH5AD` to distinguish FVF methods
+- Fixes to UpdateSeuratObject for v2 objects
+- Sink all output from stdout to stderr
+- Fix to scale.data cell ordering after subsetting 
+- Enable `Assay` specification in `BuildClusterTree`
+- Fix `FeaturePlot` when using both `blend` and `split.by`
+- Fix to `WhichCells` when passing `cells` and `invert`
+- Fix to `HoverLocator` labels and title
+- Ensure features names don't contain pipes (`|`)
+- Deprecation of `RunLSI` and `RunALRA`
+- Fix legend bug when sorting in `ExIPlot`
+
 ## [3.0.2] - 2019-06-07
 ### Added
 - Flag to skip singleton grouping in `FindClusters`

R/RcppExports.R

@@ -21,10 +21,6 @@ LogNorm <- function(data, scale_factor, display_progress = TRUE) {
     .Call('_Seurat_LogNorm', PACKAGE = 'Seurat', data, scale_factor, display_progress)
 }
 
-FastMatMult <- function(m1, m2) {
-    .Call('_Seurat_FastMatMult', PACKAGE = 'Seurat', m1, m2)
-}
-
 FastRowScale <- function(mat, scale = TRUE, center = TRUE, scale_max = 10, display_progress = TRUE) {
     .Call('_Seurat_FastRowScale', PACKAGE = 'Seurat', mat, scale, center, scale_max, display_progress)
 }