Dev jg 0701 Show Diffs

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ArchR
 Type: Package
-Date: 2022-04-03
+Date: 2022-07-17
 Title: Analyzing single-cell regulatory chromatin in R.
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: c(
     person("Jeffrey", "Granja", email = "[email protected]", role = c("aut","cre")),
     person("Ryan", "Corces", role = "aut"))
@@ -14,6 +14,7 @@ LazyData: TRUE
 RoxygenNote: 7.1.2
 Encoding: UTF-8
 Imports:
+    devtools,
     ggplot2,
     SummarizedExperiment,
     data.table,
@@ -83,6 +84,7 @@ Collate:
     'RNAIntegration.R'
     'RcppExports.R'
     'ReproduciblePeakSet.R'
+    'SparseUtils.R'
     'Trajectory.R'
     'ValidationUtils.R'
     'VisualizeData.R'

NAMESPACE

@@ -9,12 +9,15 @@ export("%ni%")
 export(.DollarNames.ArchRProject)
 export(ArchRBrowser)
 export(ArchRBrowserTrack)
+export(ArchRHeatmap)
 export(ArchRPalettes)
 export(ArchRProject)
 export(addArchRAnnotations)
 export(addArchRChrPrefix)
 export(addArchRDebugging)
 export(addArchRGenome)
+export(addArchRH5Level)
+export(addArchRLocking)
 export(addArchRLogging)
 export(addArchRThreads)
 export(addArchRVerbose)
@@ -57,6 +60,7 @@ export(createArrowFiles)
 export(createGeneAnnotation)
 export(createGenomeAnnotation)
 export(createLogFile)
+export(customEnrichment)
 export(enrichHeatmap)
 export(exportGroupSE)
 export(exportPeakMatrixForSTREAM)
@@ -67,6 +71,7 @@ export(findMacs2)
 export(getArchRChrPrefix)
 export(getArchRDebugging)
 export(getArchRGenome)
+export(getArchRH5Level)
 export(getArchRLogging)
 export(getArchRThreads)
 export(getArchRVerbose)
@@ -90,6 +95,7 @@ export(getGenes)
 export(getGenome)
 export(getGenomeAnnotation)
 export(getGroupBW)
+export(getGroupFragments)
 export(getGroupSE)
 export(getGroupSummary)
 export(getImputeWeights)
@@ -101,6 +107,7 @@ export(getMatrixFromArrow)
 export(getMatrixFromProject)
 export(getMonocleTrajectories)
 export(getOutputDirectory)
+export(getPBGroupSE)
 export(getPeak2GeneLinks)
 export(getPeakAnnotation)
 export(getPeakSet)
@@ -111,6 +118,7 @@ export(getSampleColData)
 export(getSampleNames)
 export(getSeqnames)
 export(getTSS)
+export(getTestArrow)
 export(getTestFragments)
 export(getTestProject)
 export(getTrajectory)
@@ -153,12 +161,14 @@ export(projectBulkATAC)
 export(recoverArchRProject)
 export(reformatFragmentFiles)
 export(saveArchRProject)
+export(setArchRLocking)
 export(subsetArchRProject)
 export(subsetCells)
 export(theme_ArchR)
 export(trajectoryHeatmap)
 export(validBSgenome)
 import(data.table)
+importClassesFrom(GenomicRanges,GRanges)
 importFrom(GenomicRanges,GRanges)
 importFrom(Rcpp,sourceCpp)
 useDynLib(ArchR)

R/AllClasses.R

@@ -1,5 +1,6 @@
 #' @useDynLib ArchR
 #' @importFrom Rcpp sourceCpp
+#' @importClassesFrom GenomicRanges GRanges
 #' @importFrom GenomicRanges GRanges
 #' @import data.table
 NULL
@@ -87,6 +88,15 @@ setMethod("show", "ArchRProject",
 #' genome information such as nucleotide information or chromosome sizes.
 #' @param showLogo A boolean value indicating whether to show the ascii ArchR logo after successful creation of an `ArchRProject`.
 #' @param threads The number of threads to use for parallel execution.
+#'
+#' @examples
+#'
+#' # Get Test Arrow
+#' arrow <- getTestArrow()
+#'
+#' # Create ArchR Project for Analysis
+#' proj <- ArchRProject(arrow)   
+#'
 #' @export
 ArchRProject <- function(
   ArrowFiles = NULL, 
@@ -209,6 +219,15 @@ ArchRProject <- function(
 #' This function will recover an ArchRProject if it has broken sampleColData or cellColData due to different versions of bioconductor s4vectors.
 #' 
 #' @param ArchRProj An `ArchRProject` object.
+#' 
+#' @examples
+#'
+#' # Get Test Project
+#' proj <- getTestProject()
+#'
+#' # Try to Recover ArchR Project
+#' proj <- recoverArchRProject(proj)
+#'
 #' @export
 recoverArchRProject <- function(ArchRProj){
 
@@ -230,6 +249,11 @@ recoverArchRProject <- function(ArchRProj){
     }
   }
 
+  #Try to make sure that DataFrame matches currently loaded
+  #S4Vectors Package
+  ArchRProj@cellColData <- DataFrame(ArchRProj@cellColData)
+  ArchRProj@sampleColData <- DataFrame(ArchRProj@sampleColData)
+
   if(inherits(ArchRProj@peakSet, "GRanges")){
 
     peakSet <- tryCatch({
@@ -355,6 +379,24 @@ recoverArchRProject <- function(ArchRProj){
 #' background peaks) should be ignored when re-normalizing file paths. If set to `FALSE` loading of the `ArchRProject`
 #' will fail unless all components can be found.
 #' @param showLogo A boolean value indicating whether to show the ascii ArchR logo after successful creation of an `ArchRProject`.
+#' 
+#' @examples
+#'
+#' # Get Small PBMC Project Location
+#' zipProj <- file.path(system.file("testdata", package="ArchR"), "PBSmall.zip")
+#'
+#' # Copy to current directory
+#' file.copy(zipProj, basename(zipProj), overwrite = TRUE)
+#' 
+#' # Unzip
+#' unzip(basename(zipProj), overwrite = TRUE)
+#' 
+#' # Remove
+#' file.remove(basename(zipProj))
+#'
+#' # Load
+#' loadArchRProject("PBSmall")
+#'
 #' @export
 loadArchRProject <- function(
   path = "./", 
@@ -482,6 +524,14 @@ loadArchRProject <- function(
 #' @param dropCells A boolean indicating whether to drop cells that are not in `ArchRProject` from corresponding Arrow Files.
 #' @param logFile The path to a file to be used for logging ArchR output.
 #' @param threads The number of threads to use for parallel execution.
+#' @examples
+#'
+#' # Get Small Test Project
+#' proj <- getTestProject()
+#'
+#' # Save
+#' saveArchRProject(proj)
+#'
 #' @export
 saveArchRProject <- function(
   ArchRProj = NULL,
@@ -617,6 +667,15 @@ saveArchRProject <- function(
 #' @param logFile The path to a file to be used for logging ArchR output.
 #' @param threads The number of threads to use for parallel execution. 
 #' @param force If output directory exists overwrite.
+#' 
+#' @examples
+#'
+#' # Get Small Test Project
+#' proj <- getTestProject()
+#' 
+#' #Subset
+#' proj <- subsetArchRProject(proj, cells = getCellNames(proj)[1:50])
+#' 
 #' @export
 subsetArchRProject <- function(
   ArchRProj = NULL,
@@ -784,7 +843,6 @@ subsetArchRProject <- function(
 
 }
 
-
 setMethod(
   f = "colnames",
   signature = c("x" = "ArchRProject"),

R/AnnotationGenome.R

@@ -10,6 +10,21 @@
 #' @param filterChr A character vector indicating the seqlevels that should be removed if manual removal is desired for certain seqlevels.
 #' If no manual removal is desired, `filterChr` should be set to `NULL`. If `filter` is set to `TRUE` but `filterChr` is set to `NULL`,
 #' non-standard chromosomes will still be removed as defined in `filterChrGR()`.
+#' 
+#' @examples
+#'
+#' if (!require("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
+#' library(BSgenome.Hsapiens.UCSC.hg19)
+#'
+#' # Get Genome
+#' genome <- BSgenome.Hsapiens.UCSC.hg19
+#'
+#' # Create Genome Annotation
+#' genomeAnno <- createGenomeAnnotation(genome)
+#' 
+#' # Also can create from a string if BSgenome exists
+#' genomeAnno <- createGenomeAnnotation("hg19")
+#'
 #' @export
 createGenomeAnnotation <- function(
   genome = NULL,
@@ -78,6 +93,27 @@ createGenomeAnnotation <- function(
 #' @param exons A `GRanges` object containing gene exon coordinates. Must have a symbols column matching the symbols column of `genes`.
 #' @param TSS A `GRanges` object containing standed transcription start site coordinates for computing TSS enrichment scores downstream.
 #' @param annoStyle annotation style to map between gene names and various gene identifiers e.g. "ENTREZID", "ENSEMBL".
+#' @param singleStrand A boolean for GenomicFeatures::genes(`single.strand.genes.only`) parameter
+#' 
+#' @examples
+#'
+#' if (!require("TxDb.Hsapiens.UCSC.hg19.knownGene", quietly = TRUE)) BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
+#' if (!require("org.Hs.eg.db", quietly = TRUE)) BiocManager::install("org.Hs.eg.db")
+#' library(TxDb.Hsapiens.UCSC.hg19.knownGene)
+#' library(org.Hs.eg.db)
+#'
+#' # Get Txdb
+#' TxDb <- TxDb.Hsapiens.UCSC.hg19.knownGene
+#'
+#' # Get OrgDb
+#' OrgDb <- org.Hs.eg.db
+#'
+#' # Create Genome Annotation
+#' geneAnno <- createGeneAnnotation(TxDb=TxDb, OrgDb=OrgDb)
+#' 
+#' # Also can create from a string if BSgenome exists
+#' geneAnno <- createGeneAnnotation("hg19")
+#'
 #' @export
 createGeneAnnotation <- function(
   genome = NULL,
@@ -86,7 +122,8 @@ createGeneAnnotation <- function(
   genes = NULL,
   exons = NULL,
   TSS = NULL,
-  annoStyle = NULL
+  annoStyle = NULL,
+  singleStrand = FALSE
   ){
 
   .validInput(input = genome, name = "genome", valid = c("character", "null"))
@@ -118,7 +155,11 @@ createGeneAnnotation <- function(
 
     ###########################
     message("Getting Genes..")
-    genes <- GenomicFeatures::genes(TxDb)
+    genes <- tryCatch({ #Legacy Catch In Case
+      GenomicFeatures::genes(TxDb, single.strand.genes.only = singleStrand)
+    }, error = function(e){
+      GenomicFeatures::genes(TxDb)
+    })
 
     if(is.null(annoStyle)){
       isEntrez <- mcols(genes)$symbol <- tryCatch({