Release 1.0.0 (GreenleafLab#376)

* updates

* Update DESCRIPTION

* documentation

* document

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* trajectory

* add trajectory and clustering params

* New additions for multi modal analysis

* documentation updates

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* bugfix

* Update README.md

* Update README.md

* threads are integer for umap

* Update README.md

* add stream trajectory export

* add empirical p-value and dims to use in integration

* typo

* add seed arguments to LSI

* fix buffer ratio

* update param addmotifannot

update param

* add getFragmentsFromProject

* update documentation

* remove default size aes in rasterized point

* added .safeSaveRDS

* add check for subsetArchRProject

* added na.rm = TRUE to validating a numeric integer

* update documentation

* add getAvailableMatrices check for getMatrixFromProject

* Update ArrowRead.R

* bugfix of rowRanges for peakmatrix not staying

* bugfix

* add a check for 0 cells

* addmodule score and imputation of cellColData

* add normMethod = "None" to browser

* update documentation

* add back size to ggplot

* bugfix multimodal cbind

* update getBlacklist

* force removeFilteredCells=TRUE

* bugfix reducedDims not passed to imputation in RNA integration

* add more logging to markerFeatures

* bugfix

* force sparse matrix for scRNA

* catch 0 overlap

* added checkSparseMatrix for getPartialMatrix

* add .checkSparseMatrix to MarkerFeatures

* update create arrow

* bugfix

* adding test genome

* testgenome

* Added PBMC Small Project

* add test fragments

* document

* update test stuff

* add logging to plotP2GHeatmap

* browser plotting order

* bugfix case in correlate matrices

* bugfix deviationsmatrix in copyarrows

* bug fix 1d bias

* update subsetting

* clarify subset message

* bugfix ncol markerSE = 1

* add message for number of overlapping gene names

* add ArchR method for background peaks

* add more logging to tile matrix

* convert to vector

* Add Raw output Peak2GeneLinks

* add cellsToUse to peak2gene links

* Update addPeak2GeneLinks.Rd

* make nLabel functional

* force archr with non-fixed width peaks

* clean groupBW and self KNN

* document

* update plotBrowserTrack to now have single cell tracks!

* Update ArchRBrowser.R

* Update ArchRBrowser.R

* Update ArchRBrowser.R

* bugfix

* cleanup

* add gene plots to browser with patchwork!

* document

* bugfix

* useMatrix = NULL

* bugfix normmetho -> normmethod

* add null to getTrajectory

* update plotFragSizes and plotTSS to have groupBy option

* file locking

* statistics to coA and P2G stable

* update coaccessibility

* test

* Update auto-comment.yml

* Update auto-comment.yml

.github/auto-comment.yml

@@ -0,0 +1,6 @@
+# Comment to a new issue.
+issueOpened: >
+  Thank your for raising a issue. We will try and get back to you as soon as possible.
+
+  Please make sure you have given us as much context as possible.
+

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ArchR
 Type: Package
-Date: 2019-05-11
+Date: 2020-10-01
 Title: Analyzing single-cell regulatory chromatin in R.
-Version: 0.9.5
+Version: 1.0.0
 Authors@R: c(
     person("Jeffrey", "Granja", email = "[email protected]", role = c("aut","cre")),
     person("Ryan", "Corces", role = "aut"))
@@ -73,8 +73,11 @@ Collate:
     'MarkerFeatures.R'
     'MatrixDeviations.R'
     'MatrixFeatures.R'
+    'MatrixGeneExpression.R'
     'MatrixGeneScores.R'
     'MatrixTiles.R'
+    'ModuleScore.R'
+    'MultiModal.R'
     'ProjectMethods.R'
     'QualityControl.R'
     'RNAIntegration.R'

NAMESPACE

@@ -21,17 +21,21 @@ export(addBgdPeaks)
 export(addCellColData)
 export(addClusters)
 export(addCoAccessibility)
+export(addCombinedDims)
 export(addDemuxletResults)
 export(addDeviationsMatrix)
 export(addDoubletScores)
 export(addFeatureCounts)
 export(addFeatureMatrix)
+export(addGeneExpressionMatrix)
 export(addGeneIntegrationMatrix)
 export(addGeneScoreMatrix)
 export(addGroupCoverages)
 export(addHarmony)
 export(addImputeWeights)
 export(addIterativeLSI)
+export(addModuleScore)
+export(addMonocleTrajectory)
 export(addMotifAnnotations)
 export(addPeak2GeneLinks)
 export(addPeakAnnotations)
@@ -40,6 +44,7 @@ export(addPeakSet)
 export(addProjectSummary)
 export(addReproduciblePeakSet)
 export(addSampleColData)
+export(addSlingShotTrajectories)
 export(addTSNE)
 export(addTileMatrix)
 export(addTrajectory)
@@ -53,6 +58,7 @@ export(createGenomeAnnotation)
 export(createLogFile)
 export(enrichHeatmap)
 export(exportGroupSE)
+export(exportPeakMatrixForSTREAM)
 export(extendGR)
 export(filterChrGR)
 export(filterDoublets)
@@ -76,6 +82,7 @@ export(getExons)
 export(getFeatures)
 export(getFootprints)
 export(getFragmentsFromArrow)
+export(getFragmentsFromProject)
 export(getGeneAnnotation)
 export(getGenes)
 export(getGenome)
@@ -90,6 +97,7 @@ export(getMarkers)
 export(getMatches)
 export(getMatrixFromArrow)
 export(getMatrixFromProject)
+export(getMonocleTrajectories)
 export(getOutputDirectory)
 export(getPeak2GeneLinks)
 export(getPeakAnnotation)
@@ -101,6 +109,8 @@ export(getSampleColData)
 export(getSampleNames)
 export(getSeqnames)
 export(getTSS)
+export(getTestFragments)
+export(getTestProject)
 export(getTrajectory)
 export(getTutorialData)
 export(getValidBarcodes)
@@ -110,6 +120,7 @@ export(ggGroup)
 export(ggHex)
 export(ggOneToOne)
 export(ggPoint)
+export(import10xFeatureMatrix)
 export(imputeMatrix)
 export(installExtraPackages)
 export(loadArchRProject)

R/AllClasses.R

@@ -617,7 +617,7 @@ saveArchRProject <- function(
   }
 
   message("Saving ArchRProject...")
-  saveRDS(newProj, file.path(outputDirectory, "Save-ArchR-Project.rds"))
+  .safeSaveRDS(newProj, file.path(outputDirectory, "Save-ArchR-Project.rds"))
 
   if(load){
     message("Loading ArchRProject...")
@@ -636,14 +636,16 @@ saveArchRProject <- 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. 
+#' @param force If output directory exists overwrite.
 #' @export
 subsetArchRProject <- function(
   ArchRProj = NULL,
   cells = getCellNames(ArchRProj),
   outputDirectory = "ArchRSubset",
   dropCells = TRUE,
   logFile = NULL,
-  threads = getArchRThreads()
+  threads = getArchRThreads(),
+  force = FALSE
   ){
 
   .validInput(input = ArchRProj, name = "ArchRProj", valid = "ArchRProj")
@@ -652,6 +654,12 @@ subsetArchRProject <- function(
 
   outDirOld <- getOutputDirectory(ArchRProj)
 
+  if(dir.exists(outputDirectory)){
+    if(!force){
+      stop("outputDirectory exists! Please set force = TRUE to overwrite existing directory!")
+    }
+  }
+
   if(outputDirectory == outDirOld){
     stop("outputDirectory must be different than ArchRProj outputDirectory to properly subset!")
   }
@@ -754,12 +762,49 @@ subsetArchRProject <- function(
     i <- rownames(cD)[i]
   }
 
+  if(length(i) == 1){
+    stop("Length of subsetting cells must be greater than 1!")
+  }
+
+  i <- unique(i)
+
+  #First Subset CellColData
   x@cellColData <- cD[i, , drop=FALSE]
+  cellsKeep <- rownames(x@cellColData)
+
+  #Second Remove Impute Weights
+  if(length(i) != nrow(cD)){
+    if(length(x@imputeWeights) != 0){
+    message("Dropping ImputeWeights Since You Are Subsetting Cells! ImputeWeights is a cell-x-cell Matrix!")
+    }
+    x@imputeWeights <- SimpleList()
+  }
+
+  #Third Subset ReducedDims
+  rD <- x@reducedDims
+  rD2 <- lapply(seq_along(rD), function(x){
+    rD[[x]][[1]] <- rD[[x]][[1]][cellsKeep, , drop = FALSE]
+    rD[[x]]
+  }) %>% SimpleList()
+  names(rD2) <- names(rD)
+  rD <- x@reducedDims
+  rm(rD, rD2)
+
+  #Fourth Subset Embeddings
+  eD <- x@embeddings
+  eD2 <- lapply(seq_along(eD), function(x){
+    eD[[x]][[1]] <- eD[[x]][[1]][cellsKeep, , drop = FALSE]
+    eD[[x]]
+  }) %>% SimpleList()
+  names(eD2) <- names(eD)
+  x@embeddings <- eD2
+  rm(eD, eD2)
 
   return(x)
 
 }
 
+
 setMethod(
   f = "colnames",
   signature = c("x" = "ArchRProject"),

R/AnnotationPeaks.R

@@ -217,9 +217,9 @@ addPeakAnnotations <- function(
   ArchRProj@peakAnnotation[[name]]$Positions <- savePositions
   ArchRProj@peakAnnotation[[name]]$Matches <- saveMatches
 
-  saveRDS(out, file.path(getOutputDirectory(ArchRProj),  "Annotations", paste0(name,"-In-Peaks-Summary.rds")), compress = FALSE)
-  saveRDS(out$regionPositions, savePositions, compress = FALSE)
-  saveRDS(out$regionMatches, saveMatches, compress = FALSE)
+  .safeSaveRDS(out, file.path(getOutputDirectory(ArchRProj),  "Annotations", paste0(name,"-In-Peaks-Summary.rds")), compress = FALSE)
+  .safeSaveRDS(out$regionPositions, savePositions, compress = FALSE)
+  .safeSaveRDS(out$regionMatches, saveMatches, compress = FALSE)
 
   return(ArchRProj)
 
@@ -239,6 +239,7 @@ addPeakAnnotations <- function(
 #' used from CisBP/JASPAR. By default, this function will attempt to guess the species based on the value from `getGenome()`.
 #' @param collection If one of the JASPAR motif sets is used via `motifSet`, this parameter allows you to indicate the JASPAR
 #' collection to be used. See `getMatrixSet()` from `TFBSTools` for all options to supply for collection.
+#' @param motifPWMs A custom set of motif PWMs as a PWMList for adding motif annotations.
 #' @param cutOff The p-value cutoff to be used for motif search. The p-value is determined vs a background set of sequences
 #' (see `MOODS` for more details on this determination).
 #' @param width The width in basepairs to consider for motif matches. See the `motimatchr` package for more information.
@@ -473,9 +474,9 @@ addMotifAnnotations <- function(
   ArchRProj@peakAnnotation[[name]]$Positions <- savePositions
   ArchRProj@peakAnnotation[[name]]$Matches <- saveMatches
 
-  saveRDS(out, file.path(getOutputDirectory(ArchRProj),  "Annotations", paste0(name,"-In-Peaks-Summary.rds")), compress = FALSE)
-  saveRDS(out$motifPositions, savePositions, compress = FALSE)
-  saveRDS(out$motifMatches, saveMatches, compress = FALSE)
+  .safeSaveRDS(out, file.path(getOutputDirectory(ArchRProj),  "Annotations", paste0(name,"-In-Peaks-Summary.rds")), compress = FALSE)
+  .safeSaveRDS(out$motifPositions, savePositions, compress = FALSE)
+  .safeSaveRDS(out$motifMatches, saveMatches, compress = FALSE)
 
   .endLogging(logFile = logFile)
 
@@ -741,8 +742,8 @@ addArchRAnnotations <- function(
   ArchRProj@peakAnnotation[[name]]$Positions <- "None"
   ArchRProj@peakAnnotation[[name]]$Matches <- saveMatches
 
-  saveRDS(out, file.path(getOutputDirectory(ArchRProj),  "Annotations", paste0(name,"-In-Peaks-Summary.rds")), compress = FALSE)
-  saveRDS(out$regionMatches, saveMatches, compress = FALSE)
+  .safeSaveRDS(out, file.path(getOutputDirectory(ArchRProj),  "Annotations", paste0(name,"-In-Peaks-Summary.rds")), compress = FALSE)
+  .safeSaveRDS(out$regionMatches, saveMatches, compress = FALSE)
 
   .endLogging(logFile = logFile)