update

DESCRIPTION

@@ -3,9 +3,11 @@ Type: Package
 Date: 2019-10-17
 Title: Analyzing regulatory chromatin in R
 Version: 0.1.4
-Author: Jeffrey Granja [aut, cre], Ryan Corces [aut]
-Maintainer: Jeffrey Granja <[email protected]>
+Authors@R: c(
+    person("Jeffrey", "Granja", email = "[email protected]", role = c("aut","cre")),
+    person("Ryan", "Corces", role = "aut"))
 Description: This package is designed to streamline scATAC analyses in R.
+Roxygen: list(markdown = TRUE)
 License: GPL (>= 2)
 LinkingTo: Rcpp
 LazyData: TRUE

NAMESPACE

@@ -12,6 +12,7 @@ export(.batchlapply)
 export(.centerRollMean)
 export(.checkPath)
 export(.cleanParams)
+export(.computeKNN)
 export(.computeROC)
 export(.confusionMatrix)
 export(.fileExtension)
@@ -61,7 +62,8 @@ export(.validTxDb)
 export(ArchRPalettes)
 export(ArchRProject)
 export(ArchRRegionTrack)
-export(addBdgPeaks)
+export(addArchRThreads)
+export(addBgdPeaks)
 export(addCNVMatrix)
 export(addCellColData)
 export(addClusters)
@@ -81,21 +83,22 @@ export(addPeakSet)
 export(addProjectSummary)
 export(addReproduciblePeakSet)
 export(addSampleColData)
-export(addSeqLengths)
+export(addSeqLengthsGR)
 export(addTileMatrix)
 export(addTrajectory)
-export(columnOverlaps)
-export(computeKNN)
-export(constructGRanges)
+export(constructGR)
 export(createArrowFiles)
-export(extendGRanges)
+export(createGeneAnnnotation)
+export(createGenomeAnnotation)
+export(extendGR)
 export(filterCells)
+export(filterChrGR)
 export(filterDoublets)
 export(filterPlot)
 export(findMacs2)
-export(getAnnotation)
+export(getArchRThreads)
 export(getArrowFiles)
-export(getBdgPeaks)
+export(getBgdPeaks)
 export(getBlacklist)
 export(getCellColData)
 export(getCellNames)
@@ -114,6 +117,7 @@ export(getInputFiles)
 export(getMatches)
 export(getMatrixFromArrow)
 export(getOutputDirectory)
+export(getPeakAnnotation)
 export(getPeakSet)
 export(getPositions)
 export(getProjectSummary)
@@ -130,26 +134,27 @@ export(ggHex)
 export(ggOneToOne)
 export(ggPoint)
 export(ggViolin)
-export(keepFilteredChromosomes)
+export(loadArchRProject)
 export(markerAnnoEnrich)
 export(markerFeatures)
+export(markerGR)
 export(markerHeatmap)
 export(markerPlot)
-export(markerRanges)
-export(mergeGRanges)
+export(mergeGR)
 export(nCells)
-export(nonOverlappingGRanges)
-export(overlappingBP)
-export(overlapsMany)
+export(nOverlapGR)
+export(nonOverlappingGR)
+export(overlapsManyGR)
 export(paletteContinuous)
 export(paletteDiscrete)
 export(plotEmbedding)
 export(plotFootprints)
 export(plotGroups)
 export(plotPDF)
 export(plotTrajectory)
-export(shuffleGRanges)
-export(subsetSeqnames)
+export(saveArchRProject)
+export(shuffleGR)
+export(subsetSeqnamesGR)
 export(theme_ArchR)
 export(trajectoryHeatmap)
 importFrom(Rcpp,sourceCpp)

R/AllClasses.R

@@ -4,7 +4,6 @@ NULL
 
 setClassUnion("characterOrNull", c("character", "NULL"))
 setClassUnion("GRangesOrNull", c("GRanges", "NULL"))
-setClassUnion("matrixOrNull",members = c("dgCMatrix","NULL"))
 
 setClass("ArchRProject", 
   representation(
@@ -13,13 +12,13 @@ setClass("ArchRProject",
     sampleColData = "DataFrame",
     sampleMetadata = "SimpleList",
     cellColData = "DataFrame", 
-    cellMetadata = "SimpleList", #Where clustering output will go to
-    reducedDims = "SimpleList", #Where clustering output will go to
-    embeddings = "SimpleList", #Where clustering output will go to
+    cellMetadata = "SimpleList", 
+    reducedDims = "SimpleList",
+    embeddings = "SimpleList",
     peakSet = "GRangesOrNull",
-    annotations = "SimpleList", #MotifMatches ETC go here
-    geneAnnotation = "SimpleList", #genes exons TSS
-    genomeAnnotation = "SimpleList", #genome chromSizes BSgenome blacklist
+    peakAnnotation = "SimpleList",
+    geneAnnotation = "SimpleList",
+    genomeAnnotation = "SimpleList",
     imputeWeights = "SimpleList"
   )
 )
@@ -44,15 +43,25 @@ setMethod("show", "ArchRProject",
   }
 )
 
+#' Create ArchRProject from ArrowFiles
+#' 
+#' This function will create an ArchRProject with given ArrowFiles.
+#'
+#' @param ArrowFiles A character vector containing the names of ArrowFiles to be used.
+#' @param outputDirectory A name for the relative path of the outputDirectory for ArchR results 
+#' @param copyArrows A boolean indicating whether ArrowFiles should be copied into outputDirectory
+#' @param geneAnno The geneAnnotation (see createGeneAnnotation) is used for downstream analyses such as calculate TSS Enrichment Scores, Gene Scores, etc.
+#' @param genomeAnno The genomeAnnotation (see createGenomeAnnotation) is used for downstream analyses for genome information such as nucleotide information or chromosome sizes.
+#' @param showLogo A boolean indicating whether to show ArchR Logo after successful creation of an ArchRProject.
 #' @export
 ArchRProject <- function(
-  ArrowFiles=NULL, 
-  sampleNames=NULL, 
-  outputDirectory = "ArchR_Results", 
+  ArrowFiles = NULL, 
+  outputDirectory = "ArchR_Output", 
   copyArrows = FALSE,
   geneAnnotation = NULL,
   genomeAnnotation = NULL,
-  showLogo = TRUE){
+  showLogo = TRUE
+  ){
 
   if(is.null(ArrowFiles)){
     stop("Need to Provide Arrow Files!")
@@ -62,10 +71,8 @@ ArchRProject <- function(
   message("Validating Arrows...")
   ArrowFiles <- unlist(lapply(ArrowFiles, .validArrow))
 
-  if(is.null(sampleNames)){
-    message("Getting SampleNames...")
-    sampleNames <- unlist(lapply(seq_along(ArrowFiles), function(x) .sampleName(ArrowFiles[x])))
-  }
+  message("Getting SampleNames...")
+  sampleNames <- unlist(lapply(seq_along(ArrowFiles), function(x) .sampleName(ArrowFiles[x])))
 
   if(any(duplicated(sampleNames))){
     stop("Error cannot have duplicate sampleNames, please add sampleNames that will overwrite the current sample name in Arrow file!")
@@ -74,7 +81,7 @@ ArchRProject <- function(
   if(length(sampleNames) != length(ArrowFiles)) stop("Samples is not equal to input ArrowFiles!")
 
   dir.create(outputDirectory,showWarnings=FALSE)
-  sampleDirectory <- file.path(normalizePath(outputDirectory),"InputArrows")
+  sampleDirectory <- file.path(normalizePath(outputDirectory), "ArrowFiles")
   dir.create(sampleDirectory,showWarnings=FALSE)
 
   if(copyArrows){
@@ -102,9 +109,12 @@ ArchRProject <- function(
     cellMetadata = SimpleList(),
     reducedDims = SimpleList(),
     embeddings = SimpleList(),
-    annotations = SimpleList(),
+    peakSet = NULL,
+    peakAnnotation = SimpleList(),
     geneAnnotation = geneAnnotation,
-    genomeAnnotation = genomeAnnotation)
+    genomeAnnotation = genomeAnnotation
+  )
+
   if(showLogo){
     .ArchRLogo(ascii = "Logo") 
   }
@@ -115,3 +125,163 @@ ArchRProject <- function(
 
 }
 
+#Validity
+.validArchRProject <- function(ArchRProj, ...){
+  if(!inherits(ArchRProj, "ArchRProject")){
+    stop("Not a valid ArchRProject as input!")
+  }else{
+    ArchRProj
+  }
+}
+
+#' Save ArchRProject for Later Usage
+#' 
+#' This function will organize arrows and project output into a directory and save the ArchRProject for later usage.
+#' 
+#' @param ArchRProj An `ArchRProject` object.
+#' @param copyArrows A boolean indicating whether to copy or copy + remove original ArrowFiles prior to saving ArchRProject.
+#' @export
+saveArchRProject <- function(
+  ArchRProj = NULL, 
+  copyArrows = TRUE
+  ){
+
+  outputDir <- getOutputDirectory(ArchRProj)
+
+  #Set Up Arrow Files
+  ArrowDir <- file.path(basename(outputDir), "ArrowFiles")
+  dir.create(ArrowDir, showWarnings = FALSE)
+
+  ArrowFiles <- getArrowFiles(ArchRProj)
+  ArrowFilesNew <- file.path(ArrowDir, basename(ArrowFiles))
+  names(ArrowFilesNew) <- names(ArrowFiles)
+
+  for(i in seq_along(ArrowFiles)){
+    cf <- file.copy(ArrowFiles[i], ArrowFilesNew[i])
+    if(!copyArrows){
+      file.remove(ArrowFiles[i])
+    }
+  }
+
+  ArchRProj@sampleColData$ArrowFiles <- ArrowFilesNew[rownames(ArchRProj@sampleColData)]
+
+  saveRDS(ArchRProj, file.path(outputDir, "Save-ArchR-Project.rds"))
+
+}
+
+#' Load Previous ArchRProject into R
+#' 
+#' This function will load a previously saved ArchRProject and re-normalize paths for usage.
+#' 
+#' @param path A character path to an ArchRProject directory that was previously saved.
+#' @param force A boolean indicating when re-normalizing paths if an annotation/bdgPeaks is not found ignore and continue
+#' @param showLogo show ArchRLogo upon completion.
+#' @export
+loadArchRProject <- function(
+  path = "./", 
+  force = FALSE, 
+  showLogo = TRUE
+  ){
+
+  path2Proj <- file.path(path, "Save-ArchR-Project.rds")
+
+  if(!file.exists(path2Proj)){
+    stop("Could not find previously saved ArchRProject in the path specified!")
+  }
+
+  ArchRProj <- readRDS(path2Proj)
+
+  outputDir <- getOutputDirectory(ArchRProj)
+  outputDirNew <- normalizePath(path)
+
+  #1. Arrows Paths
+  ArrowFilesNew <- file.path(outputDirNew, gsub(paste0(basename(outputDir),"/"),"",ArchRProj@sampleColData$ArrowFiles))
+  if(!all(file.exists(ArrowFilesNew))){
+    stop("ArrowFiles do not exist in saved ArchRProject!")
+  }
+  ArchRProj@sampleColData$ArrowFiles <- ArrowFilesNew
+
+  #2. Annotations Paths
+
+  if(length(ArchRProj@peakAnnotation) > 0){
+
+    keepAnno <- rep(TRUE, length(ArchRProj@peakAnnotation))
+
+    for(i in seq_along(ArchRProj@peakAnnotation)){
+      #Postions
+      if(!is.null(ArchRProj@peakAnnotation[[i]]$Positions)){
+
+        PositionsNew <- gsub(outputDir, outputDirNew, ArchRProj@peakAnnotation[[i]]$Positions)
+        if(!all(file.exists(PositionsNew))){
+          if(force){
+            keepAnno[i] <- FALSE
+            message("Positions for peakAnnotation do not exist in saved ArchRProject!")
+          }else{
+            stop("Positions for peakAnnotation do not exist in saved ArchRProject!")
+          }
+        }
+        ArchRProj@peakAnnotation[[i]]$Positions <- PositionsNew
+
+      }
+
+      #Matches
+      if(!is.null(ArchRProj@peakAnnotation[[i]]$Matches)){
+
+        MatchesNew <- gsub(outputDir, outputDirNew, ArchRProj@peakAnnotation[[i]]$Matches)
+        if(!all(file.exists(MatchesNew))){
+          if(force){
+            message("Matches for peakAnnotation do not exist in saved ArchRProject!")
+            keepAnno[i] <- FALSE
+          }else{
+            stop("Matches for peakAnnotation do not exist in saved ArchRProject!")
+          }
+        }
+        ArchRProj@peakAnnotation[[i]]$Matches <- MatchesNew
+
+      }
+
+    }
+
+    ArchRProj@peakAnnotation <- ArchRProj@peakAnnotation[keepAnno]
+
+  }
+
+
+  #3. Background Peaks Paths
+  if(!is.null(getPeakSet(ArchRProj))){
+
+    if(!is.null(metadata(getPeakSet(ArchRProj))$bgdPeaks)){
+
+      bgdPeaksNew <- gsub(outputDir, outputDirNew, metadata(getPeakSet(ArchRProj))$bgdPeaks)
+
+      if(!all(file.exists(bgdPeaksNew))){
+
+        if(force){
+          message("BackgroundPeaks do not exist in saved ArchRProject!")
+          metadata(ArchRProj@peakSet)$bgdPeaks <- NULL
+        }else{
+          stop("BackgroundPeaks do not exist in saved ArchRProject!")
+        }
+
+      }else{
+
+        metadata(ArchRProj@peakSet)$bgdPeaks <- bgdPeaksNew
+
+      }    
+
+    }
+
+  }
+
+  #4. Set Output Directory 
+
+  ArchRProj@projectMetadata$outputDirectory <- outputDirNew
+
+  message("Successfully loaded ArchRProject!")
+  if(showLogo){
+      .ArchRLogo(ascii = "Logo")
+  }  
+
+  ArchRProj
+
+}