Merge branch 'develop'

Author: timoast

.Rbuildignore

@@ -17,3 +17,4 @@ index.*
 Dockerfile
 ^CRAN-RELEASE$
 benchmark/
+.dockerignore

.dockerignore

@@ -0,0 +1 @@
+*

.github/ISSUE_TEMPLATE/--documentation.md

@@ -1,10 +1,10 @@
 ---
 name: "\U0001F4DADocumentation"
-about: An issue related to https://satijalab.org/signac/
+about: An issue related to Signac documentation
 title: ''
 labels: documentation
 assignees: ''
 
 ---
 
-<!-- A clear description of what content at https://satijalab.org/signac or in the Signac function man pages is an issue. -->
+<!-- A clear description of what content at the Signac website or in the Signac function man pages is an issue. -->

.github/ISSUE_TEMPLATE/bug_report.md

@@ -7,7 +7,7 @@ assignees: ''
 
 ---
 
-<!-- Briefly describe your problem and what output you expect. If you have a question, please use the analysis question template instead. -->
+<!-- Briefly describe your problem and what output you expect. If you have a question, please open a discussion topic instead. -->
 
 <!-- Before posting an issue, ensure that the bug is reproducible by re-running the code that produced the issue in a new R session.-->
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Signac
 Title: Analysis of Single-Cell Chromatin Data
-Version: 1.6.0
-Date: 2022-03-04
+Version: 1.7.0
+Date: 2022-05-31
 Authors@R: c(
   person(given = 'Tim', family = 'Stuart', email = '[email protected]', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3044-0897')),
   person(given = 'Avi', family = 'Srivastava', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-9798-2079')),
@@ -24,38 +24,33 @@ URL: https://github.com/timoast/signac, https://satijalab.org/signac
 BugReports: https://github.com/timoast/signac/issues
 LinkingTo: Rcpp
 Imports: 
-    GenomeInfoDb,
+    GenomeInfoDb (>= 1.29.3),
     GenomicRanges,
     IRanges,
     Matrix,
     Rsamtools,
     S4Vectors,
-    Seurat (>= 4.0.6),
     SeuratObject (>= 4.0.0),
     data.table,
     dplyr (>= 1.0.0),
     future,
     future.apply,
     ggplot2,
-    ggseqlogo,
     irlba,
     pbapply,
     tidyr,
     patchwork,
     stats,
     utils,
     BiocGenerics,
-    ggrepel,
     stringi,
     fastmatch,
-    lsa,
     RcppRoll,
     scales,
     Rcpp,
-    ggforce,
-    qlcMatrix,
     grid,
-    tidyselect
+    tidyselect,
+    vctrs
 Collate: 
     'RcppExports.R'
     'data.R'
@@ -80,6 +75,10 @@ Collate:
     'visualization.R'
     'zzz.R'
 Suggests: 
+    Seurat (>= 4.0.6),
+    ggforce,
+    ggrepel,
+    ggseqlogo,
     testthat (>= 2.1.0),
     chromVAR,
     SummarizedExperiment,
@@ -90,4 +89,6 @@ Suggests:
     miniUI,
     rtracklayer,
     biovizBase,
-    Biostrings
+    Biostrings,
+    lsa,
+    qlcMatrix

Dockerfile

@@ -1,18 +1,7 @@
 FROM satijalab/seurat:latest
 
-# Install system dependencies
 RUN apt-get update --fix-missing \
-  && apt-get install -y software-properties-common \
-  && add-apt-repository -y ppa:git-core/ppa \
-  && apt-get update \
-  && apt-get install -y git libbz2-dev liblzma-dev
-
-# Install Bioconductor dependencies
-
-RUN R --slave --no-restore --no-save -e "install.packages('BiocManager'); BiocManager::install(c('GenomeInfoDbData', 'GO.db'))"
-
-# Install Signac
-
-RUN  R --slave --no-restore --no-save -e "setRepositories(ind=1:2); install.packages('Signac',  repos = c('https://cloud.r-project.org', 'https://bioconductor.org/packages/3.13/bioc'),dependencies = TRUE)"
+  && apt-get install -y libbz2-dev liblzma-dev \
+  &&  R --slave --no-restore --no-save -e "options(repos=c(CRAN='https://cloud.r-project.org')); setRepositories(ind=1:3); install.packages('Signac', dependencies = TRUE)"
 
 CMD [ "R" ]

NAMESPACE

@@ -10,6 +10,7 @@ S3method("Links<-",Seurat)
 S3method("Motifs<-",ChromatinAssay)
 S3method("Motifs<-",Seurat)
 S3method("[",Motif)
+S3method(AddMotifs,Assay)
 S3method(AddMotifs,ChromatinAssay)
 S3method(AddMotifs,Seurat)
 S3method(AddMotifs,default)
@@ -29,14 +30,14 @@ S3method(CallPeaks,Fragment)
 S3method(CallPeaks,Seurat)
 S3method(CallPeaks,default)
 S3method(Cells,Fragment)
+S3method(ConvertMotifID,Assay)
 S3method(ConvertMotifID,ChromatinAssay)
 S3method(ConvertMotifID,Motif)
 S3method(ConvertMotifID,Seurat)
 S3method(ConvertMotifID,default)
 S3method(FindTopFeatures,Assay)
 S3method(FindTopFeatures,Seurat)
 S3method(FindTopFeatures,default)
-S3method(FoldChange,ChromatinAssay)
 S3method(Footprint,ChromatinAssay)
 S3method(Footprint,Seurat)
 S3method(Fragments,ChromatinAssay)
@@ -122,7 +123,6 @@ export(FilterCells)
 export(FindClonotypes)
 export(FindMotifs)
 export(FindTopFeatures)
-export(FoldChange)
 export(Footprint)
 export(FractionCountsInRegion)
 export(FragmentHistogram)
@@ -209,7 +209,7 @@ exportMethods(seqnames)
 import(data.table)
 import(patchwork)
 importClassesFrom(Matrix,dgCMatrix)
-importClassesFrom(Seurat,Assay)
+importClassesFrom(SeuratObject,Assay)
 importFrom(BiocGenerics,end)
 importFrom(BiocGenerics,sort)
 importFrom(BiocGenerics,start)
@@ -292,28 +292,22 @@ importFrom(S4Vectors,mcols)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,split)
 importFrom(S4Vectors,subjectHits)
-importFrom(Seurat,"Idents<-")
-importFrom(Seurat,"VariableFeatures<-")
-importFrom(Seurat,AddMetaData)
-importFrom(Seurat,Cells)
-importFrom(Seurat,CreateAssayObject)
-importFrom(Seurat,CreateDimReducObject)
-importFrom(Seurat,DefaultAssay)
-importFrom(Seurat,Embeddings)
-importFrom(Seurat,FindClusters)
-importFrom(Seurat,FindNeighbors)
-importFrom(Seurat,FoldChange)
-importFrom(Seurat,GetAssay)
-importFrom(Seurat,GetAssayData)
-importFrom(Seurat,Idents)
-importFrom(Seurat,Project)
-importFrom(Seurat,RenameCells)
-importFrom(Seurat,RowMergeSparseMatrices)
-importFrom(Seurat,SetAssayData)
-importFrom(Seurat,SetQuantile)
-importFrom(Seurat,VariableFeatures)
-importFrom(Seurat,WhichCells)
+importFrom(SeuratObject,"Idents<-")
+importFrom(SeuratObject,"VariableFeatures<-")
+importFrom(SeuratObject,AddMetaData)
 importFrom(SeuratObject,Cells)
+importFrom(SeuratObject,CreateAssayObject)
+importFrom(SeuratObject,CreateDimReducObject)
+importFrom(SeuratObject,DefaultAssay)
+importFrom(SeuratObject,Embeddings)
+importFrom(SeuratObject,GetAssayData)
+importFrom(SeuratObject,Idents)
+importFrom(SeuratObject,Project)
+importFrom(SeuratObject,RenameCells)
+importFrom(SeuratObject,RowMergeSparseMatrices)
+importFrom(SeuratObject,SetAssayData)
+importFrom(SeuratObject,VariableFeatures)
+importFrom(SeuratObject,WhichCells)
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
 importFrom(dplyr,slice_sample)
@@ -323,7 +317,6 @@ importFrom(dplyr,ungroup)
 importFrom(fastmatch,fmatch)
 importFrom(future,nbrOfWorkers)
 importFrom(future.apply,future_lapply)
-importFrom(ggforce,geom_bezier)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,element_blank)
@@ -367,11 +360,8 @@ importFrom(ggplot2,xlab)
 importFrom(ggplot2,xlim)
 importFrom(ggplot2,ylab)
 importFrom(ggplot2,ylim)
-importFrom(ggrepel,geom_label_repel)
-importFrom(ggseqlogo,ggseqlogo)
 importFrom(grid,arrow)
 importFrom(irlba,irlba)
-importFrom(lsa,cosine)
 importFrom(methods,"slot<-")
 importFrom(methods,as)
 importFrom(methods,callGeneric)
@@ -387,7 +377,6 @@ importFrom(patchwork,guide_area)
 importFrom(patchwork,plot_layout)
 importFrom(patchwork,wrap_plots)
 importFrom(pbapply,pblapply)
-importFrom(qlcMatrix,corSparse)
 importFrom(scales,comma)
 importFrom(scales,hue_pal)
 importFrom(stats,approx)
@@ -397,6 +386,7 @@ importFrom(stats,dist)
 importFrom(stats,ecdf)
 importFrom(stats,hclust)
 importFrom(stats,median)
+importFrom(stats,p.adjust)
 importFrom(stats,phyper)
 importFrom(stats,pnorm)
 importFrom(stats,sd)

NEWS.md

@@ -1,3 +1,32 @@
+# Signac 1.7.0
+
+New functionality:
+
+* Added `method` parameter to `LinkPeaks()` ([@saketkc](https://github.com/saketkc); [#1030](https://github.com/timoast/signac/pull/1030))
+* Added ability to plot transcript isoforms (set `annotation="transcript"` in `CoveragePlot()`)
+* Added multiple testing correction to `FindMotifs()`, and new `p.adjust` column in output dataframe
+* Added `p.adjust.method` parameter to `FindMotifs()` to control multiple testing correction method used
+
+Bug fixes:
+
+* Fixed bug in `CallPeaks()` when project name contained whitespace ([#981](https://github.com/timoast/signac/issues/981))
+* Fixed bug in `CoveragePlot()` when `tile=TRUE`
+* Fixed bug in `InsertionBias()` that set the coordinates beyond the end of some chromosomes ([#986](https://github.com/timoast/signac/issues/986))
+* Fixed bug in `BigwigTrack()` when supplying a single bigwig file ([#1053](https://github.com/timoast/signac/issues/1053))
+* Fixed bug in `GeneActivity()` when specifying biotypes ([#1058](https://github.com/timoast/signac/issues/1058))
+* Fixed bug in `GeneActivity()` when gene name is an empty string ([#1055](https://github.com/timoast/signac/issues/1055))
+* Fixed bug in `FeatureMatrix()` when using list of Fragment objects ([#1056](https://github.com/timoast/signac/issues/1056))
+* Fixed bug in `RegionMatrix()` when running on objects containing renamed cells ([#1076](https://github.com/timoast/signac/issues/1076))
+* Fixed bug in `Footprint()` when using a FASTA file ([#1092](https://github.com/timoast/signac/issues/1092))
+* Fixed bug in `Footprint()` when using list of genomic regions ([#1098](https://github.com/timoast/signac/issues/1098))
+* Add check for invalid features in `FindMotifs()` ([#1109](https://github.com/timoast/signac/issues/1109))
+
+Other changes:
+
+* Improved error message when no fragment file is supplied in `CallPeaks()` ([#1062](https://github.com/timoast/signac/issues/1062))
+* Moved `Seurat`, `ggforce`, `ggrepel`, `ggseqlogo`, `lsa`, `qlcMatrix` to suggested packages
+* Added progress bar to `GetGRangesFromEnsDb()`
+
 # Signac 1.6.0
 
 New functionality:

R/differential_accessibility.R

@@ -1,12 +1,6 @@
-# Re-export Seurat generic
-#' @importFrom Seurat FoldChange
-#' @export
-Seurat::FoldChange
-
-#' @rdname FoldChange
-#' @export
+# dynamically exported, see zzz.R
 #' @method FoldChange ChromatinAssay
-#' @importFrom Seurat FoldChange GetAssayData
+#' @importFrom SeuratObject GetAssayData
 #' @importFrom Matrix rowMeans
 FoldChange.ChromatinAssay <- function(
   object,
@@ -20,6 +14,9 @@ FoldChange.ChromatinAssay <- function(
   base = 2,
   ...
 ) {
+  if (!requireNamespace(package = "Seurat", quietly = TRUE)) {
+    stop("Please install Seurat: install.packages('Seurat')")
+  }
   mean.fxn <-  function(x) {
     return(log(x = rowMeans(x = x) + pseudocount.use, base = base))
   }
@@ -31,7 +28,7 @@ FoldChange.ChromatinAssay <- function(
   )
   fc.name <- SetIfNull(x = fc.name, y = paste0("avg_log", base.text, "FC"))
   data <- GetAssayData(object = object, slot = slot)
-  FoldChange(
+  Seurat::FoldChange(
     object = data,
     cells.1 = cells.1,
     cells.2 = cells.2,

R/dimension_reduction.R

@@ -56,7 +56,7 @@ Jaccard <- function(x, y) {
 #'
 #' @importFrom irlba irlba
 #' @importFrom stats sd
-#' @importFrom Seurat CreateDimReducObject
+#' @importFrom SeuratObject CreateDimReducObject
 #' @importMethodsFrom Matrix t
 #'
 #' @rdname RunSVD
@@ -120,7 +120,7 @@ RunSVD.default <- function(
 #' @param features Which features to use. If NULL, use variable features
 #'
 #' @rdname RunSVD
-#' @importFrom Seurat VariableFeatures GetAssayData
+#' @importFrom SeuratObject VariableFeatures GetAssayData
 #' @export
 #' @concept dimension_reduction
 #' @method RunSVD Assay
@@ -174,7 +174,7 @@ RunSVD.Seurat <- function(
   ...
 ) {
   assay <- SetIfNull(x = assay, y = DefaultAssay(object = object))
-  assay.data <- GetAssay(object = object, assay = assay)
+  assay.data <- object[[assay]]
   reduction.data <- RunSVD(
     object = assay.data,
     assay = assay,