intial archr commit

ArchR.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

DESCRIPTION

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+Package: ArchR
+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]>
+Description: This package is designed to streamline scATAC analyses in R.
+License: GPL (>= 2)
+LinkingTo: Rcpp
+LazyData: TRUE
+RoxygenNote: 6.1.1
+Encoding: UTF-8
+Imports:
+    Rcpp (>= 0.12.16),
+    matrixStats,
+    plyr,
+    SummarizedExperiment,
+    Matrix,
+    nabor,
+    motifmatchr,
+    chromVAR,
+    uwot,
+    ggrepel,
+    Rsamtools,
+    gtable,
+    grid,
+    gridExtra,
+    Biostrings,
+    ComplexHeatmap,
+Depends:
+    ggplot2,
+    data.table,
+    rhdf5,
+    magrittr,
+    S4Vectors (>= 0.9.25),
+    BiocGenerics,
+    GenomicRanges,
+

LICENSE

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+MIT License
+
+Copyright (c) 2019 jgranja24
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export("%bcin%")
+export("%bcni%")
+export("%ni%")
+export(.ArchRLogo)
+export(.addMatToArrow)
+export(.availableCells)
+export(.availableChr)
+export(.availableSeqnames)
+export(.batchlapply)
+export(.centerRollMean)
+export(.checkPath)
+export(.computeROC)
+export(.confusionMatrix)
+export(.fileExtension)
+export(.fixPlotSize)
+export(.getAssay)
+export(.getColSums)
+export(.getFeatureDF)
+export(.getFragsFromArrow)
+export(.getGroupMatrix)
+export(.getMatFromArrow)
+export(.getMatrixValues)
+export(.getMetadata)
+export(.getPartialMatrix)
+export(.getQuantiles)
+export(.getRowSums)
+export(.groupMeans)
+export(.groupSds)
+export(.groupSums)
+export(.h5read)
+export(.initializeMat)
+export(.isProtectedArray)
+export(.mergeParams)
+export(.messageDiffTime)
+export(.normalizeCols)
+export(.nullGeneAnnotation)
+export(.nullGenomeAnnotation)
+export(.quantileCut)
+export(.requirePackage)
+export(.rowScale)
+export(.rowZscores)
+export(.safeSubset)
+export(.safelapply)
+export(.sampleName)
+export(.summarizeArrowContent)
+export(.suppressAll)
+export(.validArrow)
+export(.validBSgenome)
+export(.validGRanges)
+export(.validOrgDb)
+export(.validTxDb)
+export(ArchRProject)
+export(ArchRRegionTrack)
+export(ArchR_palettes)
+export(ComputeEmbedding)
+export(FilterCells)
+export(IdentifyClusters)
+export(IterativeLSI)
+export(VisualizeEmbedding)
+export(VisualizeGroups)
+export(addBackgroundPeaks)
+export(addCellColData)
+export(addDemuxletResults)
+export(addDeviationsMatrix)
+export(addDoubletScores)
+export(addFeatureMatrix)
+export(addGeneScoreMatrix)
+export(addGroupCoverages)
+export(addMotifAnnotations)
+export(addPeakMatrix)
+export(addPeakSet)
+export(addReproduciblePeakSet)
+export(addSampleColData)
+export(addSeqLengths)
+export(addTileMatrix)
+export(alignCellsToTrajectory)
+export(availableFeatures)
+export(columnOverlaps)
+export(computeCoAccessibility)
+export(computeKNN)
+export(computeLSI)
+export(constructGRanges)
+export(createArrowFiles)
+export(extendGRanges)
+export(featureEnrichment)
+export(getAnnotation)
+export(getArrowFiles)
+export(getBlacklist)
+export(getCellColData)
+export(getCellNames)
+export(getChromLengths)
+export(getChromSizes)
+export(getEmbedding)
+export(getExons)
+export(getFragmentsFromArrow)
+export(getGeneAnnotation)
+export(getGenes)
+export(getGenome)
+export(getGenomeAnnotation)
+export(getMatches)
+export(getMatrixFromArrow)
+export(getOutputDirectory)
+export(getPeakSet)
+export(getPositions)
+export(getReducedDims)
+export(getSampleColData)
+export(getSampleNames)
+export(getTSS)
+export(ggAlignPlots)
+export(ggHex)
+export(ggLine)
+export(ggOneToOne)
+export(ggPoint)
+export(ggViolin)
+export(keepFilteredChromosomes)
+export(markerFeatures)
+export(markerHeatmap)
+export(mergeGRanges)
+export(nonOverlappingGRanges)
+export(overlappingBP)
+export(overlapsMany)
+export(paletteContinuous)
+export(paletteDiscrete)
+export(plotFootprint)
+export(plotPDF)
+export(plotPeakCallSummary)
+export(projectLSI)
+export(shuffleGRanges)
+export(subsetSeqnames)
+export(summarizeFootprints)
+export(theme_ArchR)
+importFrom(Rcpp,sourceCpp)
+useDynLib(ArchR)

R/AllClasses.R

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+#' @useDynLib ArchR
+#' @importFrom Rcpp sourceCpp
+NULL
+
+setClassUnion("characterOrNull", c("character", "NULL"))
+setClassUnion("GRangesOrNull", c("GRanges", "NULL"))
+
+setClass("ArchRProject", 
+  representation(
+    projectMetadata = "SimpleList",
+    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
+    peakSet = "GRangesOrNull",
+    annotations = "SimpleList", #MotifMatches ETC go here
+    geneAnnotation = "SimpleList", #genes exons TSS
+    genomeAnnotation = "SimpleList" #genome chromSizes BSgenome blacklist
+  )
+)
+
+setMethod("show", "ArchRProject",
+  function(object) {
+    scat <- function(fmt, vals=character(), exdent=2, n = 5, ...){
+            vals <- ifelse(nzchar(vals), vals, "''")
+            lbls <- paste(S4Vectors:::selectSome(vals, maxToShow = n), collapse=" ")
+            txt <- sprintf(fmt, length(vals), lbls)
+            cat(strwrap(txt, exdent=exdent, ...), sep="\n")
+    }
+      .ArchRLogo(ascii = "Package")
+      cat("class:", class(object), "\n")
+      cat("outputDirectory:", object@projectMetadata$outputDirectory, "\n")
+      scat("samples(%d): %s\n", rownames(object@sampleColData))
+      scat("sampleColData names(%d): %s\n", names(object@sampleColData))
+      scat("cellColData names(%d): %s\n", names(object@cellColData))
+      scat("numberOfCells(%d): %s\n", nrow(object@cellColData))
+      scat("medianTSS(%d): %s\n", median(object@cellColData$TSSEnrichment))
+      scat("medianFrags(%d): %s\n", median(object@cellColData$nFrags))
+  }
+)
+
+#' @export
+ArchRProject <- function(
+  ArrowFiles=NULL, 
+  sampleNames=NULL, 
+  outputDirectory = "ArchR_Results", 
+  copyArrows = FALSE,
+  geneAnnotation = NULL,
+  genomeAnnotation = NULL,
+  showLogo = TRUE){
+
+  if(is.null(ArrowFiles)){
+    stop("Need to Provide Arrow Files!")
+  }
+
+  #Validate
+  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])))
+  }
+
+  if(any(duplicated(sampleNames))){
+    stop("Error cannot have duplicate sampleNames, please add sampleNames that will overwrite the current sample name in Arrow file!")
+  }
+
+  if(length(sampleNames) != length(ArrowFiles)) stop("Samples is not equal to input ArrowFiles!")
+
+  dir.create(outputDirectory,showWarnings=FALSE)
+  sampleDirectory <- file.path(normalizePath(outputDirectory),"InputArrows")
+  dir.create(sampleDirectory,showWarnings=FALSE)
+
+  if(copyArrows){
+    message("Copying ArrowFiles to Ouptut Directory!")
+    cf <- file.copy(ArrowFiles, file.path(sampleDirectory, paste0(sampleNames, ".arrow")))
+    ArrowFiles <- file.path(sampleDirectory, paste0(sampleNames, ".arrow"))
+  }
+
+  #Sample Information
+  sampleColData <- DataFrame(row.names = sampleNames, ArrowFiles = ArrowFiles)
+  sampleMetadata <- SimpleList(lapply(sampleNames, function(x) SimpleList()))
+  names(sampleMetadata) <- sampleNames
+
+  #Cell Information
+  metadataList <- lapply(ArrowFiles, .getMetadata)
+  intCols <- Reduce("intersect",lapply(metadataList,colnames))
+  cellColData <- lapply(metadataList, function(x) x[,intCols]) %>% Reduce("rbind",.)
+
+  proj <- new("ArchRProject", 
+    projectMetadata = SimpleList(outputDirectory = normalizePath(outputDirectory)),
+    sampleColData = sampleColData,
+    sampleMetadata = sampleMetadata,
+    cellColData = cellColData,
+    cellMetadata = SimpleList(),
+    reducedDims = SimpleList(),
+    embeddings = SimpleList(),
+    annotations = SimpleList(),
+    geneAnnotation = geneAnnotation,
+    genomeAnnotation = genomeAnnotation)
+  if(showLogo){
+    .ArchRLogo(ascii = "Logo") 
+  }
+  proj
+
+}
+