Merge branch 'develop' into set_defaults

.github/workflows/cmd-check.yml

@@ -54,7 +54,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.posit.co/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.posit.co/cran/__linux__/focal/latest" }
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -112,7 +112,7 @@ jobs:
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
         run: |
-          sysreqs=$(Rscript -e 'Sys.setenv(RSPM_ROOT = "https://packagemanager.posit.co"); cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
+          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
           echo $sysreqs
           sudo -s eval "$sysreqs"
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Signac
 Title: Analysis of Single-Cell Chromatin Data
-Version: 1.10.0
-Date: 2023-05-26
+Version: 1.14.9002
+Date: 2025-01-16
 Authors@R: c(
   person(given = 'Tim', family = 'Stuart', email = 'stuartt@gis.a-star.edu.sg', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3044-0897')),
   person(given = 'Avi', family = 'Srivastava', email = 'asrivastava@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9798-2079')),
@@ -14,12 +14,12 @@ Description: A framework for the analysis and exploration of single-cell chromat
     and normalization, visualization, and DNA sequence motif analysis.
     Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
 Depends:
-    R (>= 4.0.0),
+    R (>= 4.1.0),
     methods
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 URL: https://github.com/stuart-lab/signac, https://stuartlab.org/signac
 BugReports: https://github.com/stuart-lab/signac/issues
 LinkingTo: Rcpp
@@ -30,7 +30,7 @@ Imports:
     Matrix,
     Rsamtools,
     S4Vectors,
-    SeuratObject (>= 4.0.0),
+    SeuratObject (>= 5.0.2),
     data.table,
     dplyr (>= 1.0.0),
     future,
@@ -52,7 +52,8 @@ Imports:
     grid,
     tidyselect,
     vctrs,
-    rtracklayer
+    rtracklayer,
+    lifecycle
 Collate: 
     'RcppExports.R'
     'data.R'
@@ -77,7 +78,7 @@ Collate:
     'visualization.R'
     'zzz.R'
 Suggests: 
-    Seurat (>= 4.0.6),
+    Seurat (>= 5.0.2),
     ggforce,
     ggrepel,
     ggseqlogo,
@@ -92,5 +93,4 @@ Suggests:
     biovizBase,
     Biostrings,
     lsa,
-    qlcMatrix,
     MASS

Dockerfile

@@ -1,4 +1,4 @@
-FROM satijalab/seurat:latest
+FROM satijalab/seurat:5.0.0
 
 RUN apt-get update --fix-missing \
   && apt-get install -y libbz2-dev liblzma-dev \

NAMESPACE

@@ -5,6 +5,7 @@ S3method("Annotation<-",Seurat)
 S3method("Cells<-",Fragment)
 S3method("Fragments<-",ChromatinAssay)
 S3method("Fragments<-",Seurat)
+S3method("LayerData<-",ChromatinAssay)
 S3method("Links<-",ChromatinAssay)
 S3method("Links<-",Seurat)
 S3method("Motifs<-",ChromatinAssay)
@@ -13,12 +14,14 @@ S3method("[",Motif)
 S3method(AddMotifs,Assay)
 S3method(AddMotifs,ChromatinAssay)
 S3method(AddMotifs,Seurat)
+S3method(AddMotifs,StdAssay)
 S3method(AddMotifs,default)
 S3method(AggregateTiles,ChromatinAssay)
 S3method(AggregateTiles,Seurat)
 S3method(AggregateTiles,default)
 S3method(AlleleFreq,Assay)
 S3method(AlleleFreq,Seurat)
+S3method(AlleleFreq,StdAssay)
 S3method(AlleleFreq,default)
 S3method(Annotation,ChromatinAssay)
 S3method(Annotation,Seurat)
@@ -34,9 +37,11 @@ S3method(ConvertMotifID,Assay)
 S3method(ConvertMotifID,ChromatinAssay)
 S3method(ConvertMotifID,Motif)
 S3method(ConvertMotifID,Seurat)
+S3method(ConvertMotifID,StdAssay)
 S3method(ConvertMotifID,default)
 S3method(FindTopFeatures,Assay)
 S3method(FindTopFeatures,Seurat)
+S3method(FindTopFeatures,StdAssay)
 S3method(FindTopFeatures,default)
 S3method(Footprint,ChromatinAssay)
 S3method(Footprint,Seurat)
@@ -48,9 +53,11 @@ S3method(GetMotifData,Motif)
 S3method(GetMotifData,Seurat)
 S3method(IdentifyVariants,Assay)
 S3method(IdentifyVariants,Seurat)
+S3method(IdentifyVariants,StdAssay)
 S3method(IdentifyVariants,default)
 S3method(InsertionBias,ChromatinAssay)
 S3method(InsertionBias,Seurat)
+S3method(LayerData,ChromatinAssay)
 S3method(Links,ChromatinAssay)
 S3method(Links,Seurat)
 S3method(Motifs,ChromatinAssay)
@@ -67,9 +74,11 @@ S3method(RunChromVAR,ChromatinAssay)
 S3method(RunChromVAR,Seurat)
 S3method(RunSVD,Assay)
 S3method(RunSVD,Seurat)
+S3method(RunSVD,StdAssay)
 S3method(RunSVD,default)
 S3method(RunTFIDF,Assay)
 S3method(RunTFIDF,Seurat)
+S3method(RunTFIDF,StdAssay)
 S3method(RunTFIDF,default)
 S3method(SetAssayData,ChromatinAssay)
 S3method(SetMotifData,ChromatinAssay)
@@ -166,6 +175,7 @@ export(RunChromVAR)
 export(RunSVD)
 export(RunTFIDF)
 export(SetMotifData)
+export(SortIdents)
 export(SplitFragments)
 export(StringToGRanges)
 export(SubsetMatrix)
@@ -179,6 +189,7 @@ export(ValidateFragments)
 export(ValidateHash)
 export(VariantPlot)
 export(as.ChromatinAssay)
+export(corSparse)
 export(theme_browser)
 exportClasses(ChromatinAssay)
 exportClasses(Fragment)
@@ -300,15 +311,23 @@ importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,split)
 importFrom(S4Vectors,subjectHits)
 importFrom(SeuratObject,"Idents<-")
+importFrom(SeuratObject,"Key<-")
+importFrom(SeuratObject,"LayerData<-")
 importFrom(SeuratObject,"VariableFeatures<-")
 importFrom(SeuratObject,AddMetaData)
+importFrom(SeuratObject,Assays)
 importFrom(SeuratObject,Cells)
+importFrom(SeuratObject,CheckFeaturesNames)
 importFrom(SeuratObject,CreateAssayObject)
 importFrom(SeuratObject,CreateDimReducObject)
+importFrom(SeuratObject,CreateSeuratObject)
 importFrom(SeuratObject,DefaultAssay)
 importFrom(SeuratObject,Embeddings)
 importFrom(SeuratObject,GetAssayData)
 importFrom(SeuratObject,Idents)
+importFrom(SeuratObject,Key)
+importFrom(SeuratObject,LayerData)
+importFrom(SeuratObject,Layers)
 importFrom(SeuratObject,Project)
 importFrom(SeuratObject,RenameCells)
 importFrom(SeuratObject,RowMergeSparseMatrices)
@@ -373,6 +392,8 @@ importFrom(ggplot2,ylab)
 importFrom(ggplot2,ylim)
 importFrom(grid,arrow)
 importFrom(irlba,irlba)
+importFrom(lifecycle,deprecated)
+importFrom(lifecycle,is_present)
 importFrom(methods,"slot<-")
 importFrom(methods,as)
 importFrom(methods,callGeneric)
@@ -401,6 +422,7 @@ importFrom(stats,dist)
 importFrom(stats,ecdf)
 importFrom(stats,hclust)
 importFrom(stats,median)
+importFrom(stats,na.omit)
 importFrom(stats,p.adjust)
 importFrom(stats,phyper)
 importFrom(stats,pnorm)
@@ -414,6 +436,7 @@ importFrom(tools,file_ext)
 importFrom(tools,md5sum)
 importFrom(utils,globalVariables)
 importFrom(utils,head)
+importFrom(utils,packageVersion)
 importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
@@ -425,6 +448,7 @@ importMethodsFrom(GenomicRanges,seqnames)
 importMethodsFrom(GenomicRanges,start)
 importMethodsFrom(GenomicRanges,strand)
 importMethodsFrom(GenomicRanges,width)
+importMethodsFrom(Matrix,colMeans)
 importMethodsFrom(Matrix,mean)
 importMethodsFrom(Matrix,t)
 useDynLib(Signac)

NEWS.md

@@ -1,3 +1,67 @@
+# Unreleased
+
+Other changes:
+
+* Improve error messages for `FindMotifs()` ([#1788](https://github.com/stuart-lab/signac/issues/1788))
+* Add documentation about the required format for gene annotations, and ensure this format is present when creating the assay ([#1797](https://github.com/stuart-lab/signac/pull/1797); [@lldelisle](https://github.com/lldelisle))
+
+# Signac 1.14.0
+
+New features:
+
+* Added `SortIdents()` function to automatically order cell metadata according
+to similarity ([@JavenTyr](https://github.com/JavenTyr))
+
+Other changes:
+
+* Change to SeuratObject v5.0.2 dependency
+* Increase R dependency to 4.1
+* Deprecate `CoverageBrowser()`
+* Add informative error message for `ClosestFeature()` when gene annotations are not present in the object ([#1681](https://github.com/stuart-lab/signac/issues/1681))
+* Fix error in `CreateChromatinAssay()` when supplying a pre-computed Motif object ([#1657](https://github.com/stuart-lab/signac/issues/1657))
+* Fix error in `CoveragePlot()` when combining `cells` and `group.by` parameters ([#1724](https://github.com/stuart-lab/signac/issues/1724))
+* Added warning in `FeatureMatrix()` when requested features are on seqnames not
+present in the fragment file ([#1754](https://github.com/stuart-lab/signac/issues/1754))
+
+# Signac 1.13.0
+
+Bug fixes:
+
+* Fix bug in `SetAssayData()` for `ChromatinAssay` objects ([#1538](https://github.com/stuart-lab/signac/issues/1538))
+* Fix bug in `TSSEnrichment()` causing error on small example dataset ([#1563](https://github.com/stuart-lab/signac/issues/1563))
+* Fix errors when using a CSI index ([#1494](https://github.com/stuart-lab/signac/issues/1494))
+* Fix error in `Footprint()` when running on a small number of regions ([#1614](https://github.com/stuart-lab/signac/issues/1614))
+* Fix error in `CoveragePlot()` and `PlotFootprint()` when setting both `ident` and `split.by` parameters ([#1660](https://github.com/stuart-lab/signac/issues/1660))
+* Fix bug in `MatchRegionStats()` when NA values are present in only some of the feature metadata rows ([#1655](https://github.com/stuart-lab/signac/issues/1655))
+
+Other changes:
+
+* Add ability to plot links for certain genes only in `CoveragePlot()` ([#1459](https://github.com/stuart-lab/signac/issues/1459))
+* Add `corSparse()`, remove qlcMatrix from suggested packages ([#1570](https://github.com/stuart-lab/signac/issues/1570)) 
+* Update documentation for `GetLinkedPeaks()` and `GetLinkedGenes()` ([#1654](https://github.com/stuart-lab/signac/issues/1654))
+
+# Signac 1.12.0
+
+Bug fixes:
+
+* Fixed bug in fragment file filtering with `FilterCells()` ([#1509](https://github.com/stuart-lab/signac/issues/1509))
+
+Other changes:
+
+* Add support for SeuratObject v5
+
+# Signac 1.11.0
+
+Bug fixes:
+
+* Fix error when supplying genome string to `AddMotifs()` function ([#1437](https://github.com/stuart-lab/signac/issues/1437))
+* Fix error in quantification with multiple fragment files ([#1474](https://github.com/stuart-lab/signac/issues/1474))
+
+Other changes:
+
+* Added `region_extension` parameter to `TSSEnrichment()` function to enable changing the size of the region used to compute TSS enrichment scores ([#1444](https://github.com/stuart-lab/signac/pull/1402); @twmcart)
+* Allow fragment files with a CSI index ([#1494](https://github.com/stuart-lab/signac/issues/1494))
+
 # Signac 1.10.0
 
 New functionality:
@@ -7,7 +71,7 @@ New functionality:
 
 Bug fixes:
 
-* Fixed error in `GetReadsInRegion()` when no fragments present that overlap the region (@rockweiler; [#1348](https://github.com/stuart-lab/signac/pull/1348))
+* Fixed error in `GetReadsInRegion()` when no fragments present that overlap the region (@nrockweiler; [#1348](https://github.com/stuart-lab/signac/pull/1348))
 * Make motif names unique to avoid errors in motif-related functions ([#1311](https://github.com/stuart-lab/signac/issues/1311))
 * Ignore missing seqnames when constructing a Motif object ([#1381](https://github.com/stuart-lab/signac/issues/1381))
 * Fixed error in `BigwigTrack()` ([#1389](https://github.com/stuart-lab/signac/issues/1389))

R/differential_accessibility.R

@@ -28,7 +28,7 @@ FoldChange.ChromatinAssay <- function(
     no = base
   )
   fc.name <- SetIfNull(x = fc.name, y = paste0("avg_log", base.text, "FC"))
-  data <- GetAssayData(object = object, slot = slot)
+  data <- GetAssayData(object = object, layer = slot)
   Seurat::FoldChange(
     object = data,
     cells.1 = cells.1,

R/dimension_reduction.R

@@ -79,6 +79,12 @@ RunSVD.default <- function(
   tol = 1e-05,
   ...
 ) {
+  if (is.null(x = rownames(x = object))) {
+    rownames(x = object) <- seq_len(length.out = nrow(x = object))
+  }
+  if (is.null(x = colnames(x = object))) {
+    colnames(x = object) <- seq_len(length.out = ncol(x = object))
+  }
   n <- min(n, (ncol(x = object) - 1))
   if (verbose) {
     message("Running SVD")
@@ -128,7 +134,9 @@ RunSVD.default <- function(
 #' @concept dimension_reduction
 #' @method RunSVD Assay
 #' @examples
+#' \dontrun{
 #' RunSVD(atac_small[['peaks']])
+#' }
 RunSVD.Assay <- function(
   object,
   assay = NULL,
@@ -142,7 +150,7 @@ RunSVD.Assay <- function(
   features <- SetIfNull(x = features, y = VariableFeatures(object = object))
   data.use <- GetAssayData(
     object = object,
-    slot = "data"
+    layer = "data"
   )[features, ]
   reduction.data <- RunSVD(
     object = data.use,
@@ -157,13 +165,48 @@ RunSVD.Assay <- function(
   return(reduction.data)
 }
 
+#' @param features Which features to use. If NULL, use variable features
+#'
+#' @rdname RunSVD
+#' @importFrom SeuratObject VariableFeatures GetAssayData
+#' @export
+#' @concept dimension_reduction
+#' @method RunSVD StdAssay
+#' @examples
+#' \dontrun{
+#' RunSVD(atac_small[['peaks']])
+#' }
+RunSVD.StdAssay <- function(
+    object,
+    assay = NULL,
+    features = NULL,
+    n = 50,
+    reduction.key = "LSI_",
+    scale.max = NULL,
+    verbose = TRUE,
+    ...
+) {
+  RunSVD.Assay(
+    object = object,
+    assay = assay,
+    features = features,
+    n = n,
+    reduction.key = reduction.key,
+    scale.max = scale.max,
+    verbose = verbose,
+    ...
+  )
+}
+
 #' @param reduction.name Name for stored dimension reduction object.
 #' Default 'svd'
 #' @rdname RunSVD
 #' @export
 #' @concept dimension_reduction
 #' @examples
+#' \dontrun{
 #' RunSVD(atac_small)
+#' }
 #' @method RunSVD Seurat
 RunSVD.Seurat <- function(
   object,