Update with testing and bug fixes

DESCRIPTION

@@ -14,6 +14,7 @@ LazyData: TRUE
 RoxygenNote: 7.1.2
 Encoding: UTF-8
 Imports:
+    devtools,
     ggplot2,
     SummarizedExperiment,
     data.table,

NAMESPACE

@@ -15,6 +15,7 @@ export(addArchRAnnotations)
 export(addArchRChrPrefix)
 export(addArchRDebugging)
 export(addArchRGenome)
+export(addArchRH5Level)
 export(addArchRLocking)
 export(addArchRLogging)
 export(addArchRThreads)
@@ -68,6 +69,7 @@ export(findMacs2)
 export(getArchRChrPrefix)
 export(getArchRDebugging)
 export(getArchRGenome)
+export(getArchRH5Level)
 export(getArchRLogging)
 export(getArchRThreads)
 export(getArchRVerbose)
@@ -112,6 +114,7 @@ export(getSampleColData)
 export(getSampleNames)
 export(getSeqnames)
 export(getTSS)
+export(getTestArrow)
 export(getTestFragments)
 export(getTestProject)
 export(getTrajectory)
@@ -161,6 +164,7 @@ 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){
 
@@ -360,6 +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 = "./", 
@@ -487,6 +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,
@@ -622,6 +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,
@@ -789,7 +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({

R/AnnotationPeaks.R

@@ -8,6 +8,15 @@
 #' 
 #' @param ArchRProj An `ArchRProject` object.
 #' @param name The name of the `peakAnnotation` object (i.e. Motifs) to retrieve from the designated `ArchRProject`.
+#' 
+#' @examples
+#'
+#' # Get Test ArchR Project
+#' proj <- getTestProject()
+#'
+#' # Get Peak Annotations
+#' peakAnno <- getPeakAnnotation(proj)
+#'
 #' @export
 getPeakAnnotation <- function(ArchRProj = NULL, name = NULL){
   .validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
@@ -29,6 +38,15 @@ getPeakAnnotation <- function(ArchRProj = NULL, name = NULL){
 #' @param ArchRProj An `ArchRProject` object.
 #' @param name The name of the `peakAnnotation` object (i.e. Motifs) to retrieve from the designated `ArchRProject`.
 #' @param annoName The name of a specific annotation to subset within the `peakAnnotation`.
+#' 
+#' @examples
+#'
+#' # Get Test ArchR Project
+#' proj <- getTestProject()
+#'
+#' # Get Annotation Positions
+#' positions <- getPositions(proj)
+#'
 #' @export
 getPositions <- function(ArchRProj = NULL, name = NULL, annoName = NULL){
   .validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
@@ -65,6 +83,15 @@ getPositions <- function(ArchRProj = NULL, name = NULL, annoName = NULL){
 #' @param ArchRProj An `ArchRProject` object.
 #' @param name The name of the `peakAnnotation` object (i.e. Motifs) to retrieve from the designated `ArchRProject`.
 #' @param annoName The name of a specific annotation to subset within the `peakAnnotation`.
+#' 
+#' @examples
+#'
+#' # Get Test ArchR Project
+#' proj <- getTestProject()
+#'
+#' # Get Annotation Matches
+#' matches <- getMatches(proj)
+#'
 #' @export
 getMatches <- function(ArchRProj = NULL, name = NULL, annoName = NULL){
   .validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProj"))
@@ -104,6 +131,18 @@ getMatches <- function(ArchRProj = NULL, name = NULL, annoName = NULL){
 #' @param force A boolean value indicating whether to force the `peakAnnotation` object indicated by `name` to be overwritten
 #' if it already exists in the given `ArchRProject`.
 #' @param logFile The path to a file to be used for logging ArchR output.
+#' 
+#' @examples
+#'
+#' # Get Test ArchR Project
+#' proj <- getTestProject()
+#'
+#' # Get Motif Positions Can Be Any Interval GRanges List
+#' positions <- getPositions(proj)
+#'
+#' # Add Peak Annotations
+#' proj <- addPeakAnnotations(proj, regions = positions)
+#'
 #' @export
 addPeakAnnotations <- function(
   ArchRProj = NULL,
@@ -291,6 +330,15 @@ addPeakAnnotations <- function(
 #' it already exists in the given `ArchRProject`.
 #' @param logFile The path to a file to be used for logging ArchR output.
 #' @param ... Additional parameters to be passed to `TFBSTools::getMatrixSet` for getting a JASPAR PWM object.
+#' 
+#' @examples
+#'
+#' # Get Test ArchR Project
+#' proj <- getTestProject()
+#'
+#' # Add Motif Annotations
+#' proj <- addMotifAnnotations(proj, motifSet = "cisbptest", annoName = "test")
+#'
 #' @export
 addMotifAnnotations <- function(
   ArchRProj = NULL,
@@ -511,7 +559,11 @@ addMotifAnnotations <- function(
   # Get BSgenome Information!
   #############################################################
   genome <- ArchRProj@genomeAnnotation$genome
-  BSgenome <- eval(parse(text = genome))
+  BSgenome <- tryCatch({
+    eval(parse(text = paste0(genome)))
+  }, error = function(e){
+    eval(parse(text = paste0(genome,"::",genome)))
+  })
   BSgenome <- validBSgenome(BSgenome)
 
   #############################################################
@@ -690,6 +742,15 @@ addMotifAnnotations <- function(
 #' @param force A boolean value indicating whether to force the `peakAnnotation` object indicated by `name` to be
 #' overwritten if it already exists in the given `ArchRProject`.
 #' @param logFile The path to a file to be used for logging ArchR output.
+#' 
+#' @examples
+#'
+#' # Get Test ArchR Project
+#' proj <- getTestProject()
+#'
+#' # Add Motif Annotations
+#' proj <- addArchRAnnotations(proj, name = "test")
+#'
 #' @export
 addArchRAnnotations <- function(
   ArchRProj = NULL,
@@ -990,6 +1051,27 @@ addArchRAnnotations <- function(
 #' `cutoff` can contain any of the `assayNames` from `seMarker`.
 #' @param background A string that indicates whether to use a background set of matched peaks to compare against ("bgdPeaks") or all peaks ("all").
 #' @param logFile The path to a file to be used for logging ArchR output.
+#' 
+#' @examples
+#'
+#' # Get Test ArchR Project
+#' proj <- getTestProject()
+#'
+#' # Get Markers
+#' seMarker <- getMarkerFeatures(
+#'   ArchRProj = proj, 
+#'   useMatrix = "PeakMatrix", 
+#'   testMethod = "binomial", 
+#'   binarize = TRUE
+#' )
+#'
+#' # Get Peak Annotation Enrichment
+#' annoEnrich <- peakAnnoEnrichment(
+#'   seMarker = seMarker, 
+#'   ArchRProj = proj,
+#'   cutOff = "FDR <= 0.1 & Log2FC >= 0"
+#' )
+#'
 #' @export
 peakAnnoEnrichment <- function(
   seMarker = NULL,
@@ -1165,6 +1247,36 @@ enrichHeatmap <- function(...){
 #' @param transpose A boolean determining whether to transpose the heatmap in the plot.
 #' @param returnMatrix A boolean determining whether to return the matrix corresponding to the heatmap rather than generate a plot.
 #' @param logFile The path to a file to be used for logging ArchR output.
+#' 
+#' @examples
+#'
+#' # Get Test ArchR Project
+#' proj <- getTestProject()
+#'
+#' # Get Markers
+#' seMarker <- getMarkerFeatures(
+#'   ArchRProj = proj, 
+#'   useMatrix = "PeakMatrix", 
+#'   testMethod = "binomial", 
+#'   binarize = TRUE
+#' )
+#'
+#' # Get Peak Annotation Enrichment
+#' annoEnrich <- peakAnnoEnrichment(
+#'   seMarker = seMarker, 
+#'   ArchRProj = proj,
+#'   cutOff = "FDR <= 0.1 & Log2FC >= 0"
+#' )
+#' 
+#' # Multiply by 50 since this is a super small test sample
+#' assay(annoEnrich) <- assay(annoEnrich) * 50
+#' 
+#' #Plot
+#' p <- plotEnrichHeatmap(annoEnrich)
+#' 
+#' #PDF
+#' plotPDF(p, name = "PeakAnnoEnrich", ArchRProj = proj)
+#' 
 #' @export
 plotEnrichHeatmap <- function(
   seEnrich = NULL,