Release 1.0.1 (#542)

* bugfix remove sys.time for weird error in R 4.0

* bug fix new uwot save and loading features

* deprecated

* version number

* handle error where spurious fragments seem to be 1 tile above max

* update bugfixes

* let quantCut in plotTrajectory be null

* grepExclude in plotTrajectoryHeatmap

* bugfix integrative analysis coaccessibility and peak2genelinks

* change file locking location groupcoverages

* throw error if no peakset for adding annotations

* make it so predictionScore is not needed for peak2gene links

* update addPeakSet

* updated description

* bugfix named list

* update error handling plotEnrichHeatmap

* update error messages tilematrix

* handle error with bsgenomes

* width is end - start + 1

* bugfix checkCairo in iterativeLSI

* update archr verbosity and logging for markerfeatures

* bugfix + documentation

* update subsetting to metadata

* handling case n = 1 for deviations matrix

* bugfix ordering of scTrack

* handle error where no barcodes passing on a small chromosome/scaffold

* bugfix validBSgenome

* fix missing paren

* fix missing paren

* add feature for supplying custom gene list for rna integration

* add sanity check to partial matrix

* update cellsInArrow in case user overrides sample in ArchRProj

* Add null option for genesUse to validInput

* bugfix NA in combined vars

* add checks for genes symbol to be not a list

Co-authored-by: Ryan Corces <ryancorces@gmail.com>

Author: jgranja24

.DS_Store

@@ -1,8 +1,8 @@
 Package: ArchR
 Type: Package
-Date: 2020-10-01
+Date: 2020-11-23
 Title: Analyzing single-cell regulatory chromatin in R.
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: c(
     person("Jeffrey", "Granja", email = "jgranja.stanford@gmail.com", role = c("aut","cre")),
     person("Ryan", "Corces", role = "aut"))
@@ -11,7 +11,7 @@ Roxygen: list(markdown = TRUE)
 License: GPL (>= 2)
 LinkingTo: Rcpp
 LazyData: TRUE
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.1
 Encoding: UTF-8
 Imports:
     Rcpp (>= 0.12.16),

DESCRIPTION

@@ -17,6 +17,7 @@ export(addArchRDebugging)
 export(addArchRGenome)
 export(addArchRLogging)
 export(addArchRThreads)
+export(addArchRVerbose)
 export(addBgdPeaks)
 export(addCellColData)
 export(addClusters)
@@ -68,6 +69,7 @@ export(getArchRDebugging)
 export(getArchRGenome)
 export(getArchRLogging)
 export(getArchRThreads)
+export(getArchRVerbose)
 export(getArrowFiles)
 export(getAvailableMatrices)
 export(getBgdPeaks)

NAMESPACE

@@ -130,7 +130,7 @@ ArchRProject <- function(
 
   message("Getting SampleNames...")
   sampleNames <- unlist(.safelapply(seq_along(ArrowFiles), function(x){
-    message(x, " ", appendLF = FALSE)
+    if(getArchRVerbose()) message(x, " ", appendLF = FALSE)
     .sampleName(ArrowFiles[x])
   }, threads = threads))
   message("")
@@ -159,7 +159,7 @@ ArchRProject <- function(
   #Cell Information
   message("Getting Cell Metadata...")
   metadataList <- .safelapply(seq_along(ArrowFiles), function(x){
-    message(x, " ", appendLF = FALSE)
+    if(getArchRVerbose()) message(x, " ", appendLF = FALSE)
     .getMetadata(ArrowFiles[x])
   }, threads = threads)
   message("")

R/AllClasses.R

@@ -41,7 +41,14 @@ createGenomeAnnotation <- function(
 
     ##################
     message("Getting blacklist..")
-    blacklist <- .getBlacklist(genome = bsg@provider_version)
+
+    genomeName <- tryCatch({
+      bsg@provider_version
+    }, error = function(e){
+      strsplit(bsg@pkgname,"\\.")[[1]][4]
+    })
+
+    blacklist <- .getBlacklist(genome = genomeName)
 
   }else{
 

R/AnnotationGenome.R

@@ -98,7 +98,7 @@ getMatches <- function(ArchRProj = NULL, name = NULL, annoName = NULL){
 #' binary value is stored indicating whether each region is observed within the peak region.
 #' 
 #' @param ArchRProj An `ArchRProject` object.
-#' @param regions A `list` of `GRanges` that are to be overlapped with the `peakSet` in the `ArchRProject`.
+#' @param regions A named `list` of `GRanges` that are to be overlapped with the `peakSet` in the `ArchRProject`.
 #' @param name The name of `peakAnnotation` object to be stored as in `ArchRProject`.
 #' @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`.
@@ -136,6 +136,10 @@ addPeakAnnotations <- function(
 
   }else{
 
+    if(is.null(names(regions))){
+      names(regions) <- paste0("Region_", seq_along(regions))
+    }
+
     regionPositions <- lapply(seq_along(regions), function(x){
 
       .logThis(regions[[x]], paste0("regions[[x]]-", x), logFile = logFile)
@@ -184,6 +188,9 @@ addPeakAnnotations <- function(
   # Peak Overlap Matrix
   #############################################################
   peakSet <- getPeakSet(ArchRProj)
+  if(is.null(peakSet)){
+    .logStop("peakSet is NULL. You need a peakset to run addMotifAnnotations! See addReproduciblePeakSet!", logFile = logFile)
+  }
   allPositions <- unlist(regionPositions)
 
   .logDiffTime("Creating Peak Overlap Matrix", t1 = tstart, verbose = TRUE, logFile = logFile)
@@ -431,6 +438,9 @@ addMotifAnnotations <- function(
   #############################################################
   .logDiffTime("Finding Motif Positions with motifmatchr!", t1 = tstart, verbose = TRUE, logFile = logFile)
   peakSet <- ArchRProj@peakSet
+  if(is.null(peakSet)){
+    .logStop("peakSet is NULL. You need a peakset to run addMotifAnnotations! See addReproduciblePeakSet!", logFile = logFile)
+  }
   motifPositions <- motifmatchr::matchMotifs(
       pwms = motifs,
       subject = peakSet,
@@ -606,7 +616,11 @@ addArchRAnnotations <- function(
     }
   }
 
-  genome <- tolower(validBSgenome(getGenome(ArchRProj))@provider_version)
+  genome <- tolower(tryCatch({
+    validBSgenome(getGenome(ArchRProj))$provider_version
+  }, error = function(e){
+    strsplit(validBSgenome(getGenome(ArchRProj))@pkgname,"\\.")[[1]][4]
+  }))
 
   annoPath <- file.path(find.package("ArchR", NULL, quiet = TRUE), "data", "Annotations")
   dir.create(annoPath, showWarnings = FALSE)
@@ -690,6 +704,9 @@ addArchRAnnotations <- function(
   # Peak Overlap Matrix
   #############################################################
   peakSet <- getPeakSet(ArchRProj)
+  if(is.null(peakSet)){
+    .logStop("peakSet is NULL. You need a peakset to run addMotifAnnotations! See addReproduciblePeakSet!", logFile = logFile)
+  }
   chr <- paste0(unique(seqnames(peakSet)))
 
   .logMessage("Annotating Chromosomes", verbose = TRUE, logFile = logFile)
@@ -1061,6 +1078,10 @@ plotEnrichHeatmap <- function(
   mat <- mat[keep, ,drop = FALSE]
   .logThis(mat, "mat-mlog10Padj-Filter", logFile = logFile)
 
+  if(nrow(mat)==0){
+    stop("No enrichments found for your cutoff!")
+  }
+
   passMat <- lapply(seq_len(nrow(mat)), function(x){
     (mat[x, ] >= 0.9*max(mat[x, ])) * 1
   }) %>% Reduce("rbind", .) %>% data.frame
@@ -1070,7 +1091,7 @@ plotEnrichHeatmap <- function(
   mat[mat > pMax] <- pMax
 
   if(nrow(mat)==0){
-    stop("No enrichments found!")
+    stop("No enrichments found for your cutoff!")
   }
 
   mat <- .rowScale(as.matrix(mat), min = 0)

R/AnnotationPeaks.R

@@ -1749,6 +1749,12 @@ plotBrowserTrack <- function(
 
   title <- paste0(as.character(seqnames(region)),":", start(region)-1, "-", end(region), " ", title)
 
+  #Re-Order
+  groupDF$group2 <- factor(
+    paste0(groupDF$group2), 
+    levels = gtools::mixedsort(unique(paste0(groupDF$group2)))
+  )
+
   p <- ggplot(groupDF, aes(x=bp, y=y, width = tileSize, fill = group2, color = group2)) + 
       geom_tile(size = scTileSize) + 
       facet_grid(group2 ~ ., scales="free_y") + 

R/ArchRBrowser.R

@@ -783,6 +783,11 @@ getMatrixFromArrow <- function(
 
     matFiles <- lapply(mat, function(x) x[[2]]) %>% Reduce("c", .)
     mat <- lapply(mat, function(x) x[[1]]) %>% Reduce("cbind", .)
+    if(!all(cellNames %in% colnames(mat))){
+      .logThis(sampledCellNames, "cellNames supplied", logFile = logFile)
+      .logThis(colnames(mat), "cellNames from matrix", logFile = logFile)
+      stop("Error not all cellNames found in partialMatrix")
+    }
     mat <- mat[,sampledCellNames, drop = FALSE]
     mat <- .checkSparseMatrix(mat, length(sampledCellNames))
 
@@ -793,6 +798,11 @@ getMatrixFromArrow <- function(
   }else{
 
     mat <- Reduce("cbind", mat)
+    if(!all(cellNames %in% colnames(mat))){
+      .logThis(cellNames, "cellNames supplied", logFile = logFile)
+      .logThis(colnames(mat), "cellNames from matrix", logFile = logFile)
+      stop("Error not all cellNames found in partialMatrix")
+    }
     mat <- mat[,cellNames, drop = FALSE]
     mat <- .checkSparseMatrix(mat, length(cellNames))
 
@@ -902,6 +912,16 @@ getMatrixFromArrow <- function(
       stop("Means Variances and Ns lengths not identical")
     }
 
+    #Check if samples have NAs due to N = 1 sample or some other weird thing.
+    #Set it to min non NA variance
+    dfVars <- lapply(seq_len(nrow(dfVars)), function(x){
+      vx <- dfVars[x, ]
+      if(any(is.na(vx))){
+        vx[is.na(vx)] <- min(vx[!is.na(vx)])
+      }
+      vx
+    }) %>% Reduce("rbind", .)
+
     combinedMeans <- rowSums(t(t(dfMeans) * ns)) / sum(ns)
     summedVars <- rowSums(t(t(dfVars) * (ns - 1)) + t(t(dfMeans^2) * ns))
     combinedVars <- (summedVars - sum(ns)*combinedMeans^2)/(sum(ns)-1)
@@ -925,8 +945,6 @@ getMatrixFromArrow <- function(
     length(.availableCells(ArrowFiles[y], useMatrix))
   }) %>% unlist
 
-
-
   #Compute RowVars
   summaryDF <- .safelapply(seq_along(featureDF), function(x){
 

R/ArrowRead.R

@@ -379,10 +379,20 @@
   o <- h5createGroup(outArrow, groupName)
 
   mData <- ArrowInfo[[groupName]]
+  cellNames <- .h5read(inArrow, "Metadata/CellNames")
+  idx <- which(cellNames %in% stringr::str_split(cellsKeep, pattern="#", simplify=TRUE)[,2])
 
+  if(length(idx)==0){
+    stop("No cells matching in arrow file!")
+  }
+
   for(i in seq_len(nrow(mData))){
     h5name <- paste0(groupName, "/", mData$name[i])
-    h5write(.h5read(inArrow, h5name), file = outArrow, name = h5name)
+    mDatai <- .h5read(inArrow, h5name)
+    if(length(mDatai)==length(cellNames)){
+      mDatai <- mDatai[idx]
+    }
+    h5write(mDatai, file = outArrow, name = h5name)
   }
 
   #2. scATAC-Fragments

R/ArrowUtils.R

@@ -473,7 +473,7 @@ createArrowFiles <- function(
 
       .logDiffTime("Continuing through after error ggplot for Fragment Size Distribution", t1 = tstart, logFile = logFile)
       #print(x)
-      message("\n")
+      if(getArchRVerbose()) message("\n")
 
   })
   gc()
@@ -537,7 +537,7 @@ createArrowFiles <- function(
 
       .logDiffTime("Continuing through after error ggplot for TSS by Frags", t1 = tstart, logFile = logFile)
       #message(x)
-      message("\n")
+      if(getArchRVerbose()) message("\n")
 
   })
 
@@ -1119,7 +1119,7 @@ createArrowFiles <- function(
     TRUE
   }, error = function(x){
     tryCatch({
-      message("Attempting to index ", file," as tabix..")
+      if(getArchRVerbose()) message("Attempting to index ", file," as tabix..")
       indexTabix(file, format = "bed")
       TRUE
     }, error = function(y){
@@ -1138,7 +1138,7 @@ createArrowFiles <- function(
     }
   }, error = function(x){
     tryCatch({
-      message("Attempting to index ", file," as bam...")
+      if(getArchRVerbose()) message("Attempting to index ", file," as bam...")
       indexBam(file)
       TRUE
     }, error = function(y){
@@ -1278,7 +1278,7 @@ createArrowFiles <- function(
           o <- .suppressAll(h5createDataset(tmpFile, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
           o <- .suppressAll(h5createDataset(tmpFile, chrRGValues, storage.mode = "character", 
             dims = c(lengthRG, 1), level = 0, size = max(nchar(RG@values)) + 1))
-          o <- h5write(obj = cbind(dt$V2,dt$V3-dt$V2), file = tmpFile, name = chrPos)
+          o <- h5write(obj = cbind(dt$V2,dt$V3 - dt$V2 + 1), file = tmpFile, name = chrPos)
           o <- h5write(obj = RG@lengths, file = tmpFile, name = chrRGLengths)
           o <- h5write(obj = RG@values, file = tmpFile, name = chrRGValues)
 
@@ -1314,7 +1314,7 @@ createArrowFiles <- function(
           o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", 
             dims = c(lengthRG, 1), level = 0, size = max(nchar(RG@values)) + 1))
 
-          o <- h5write(obj = cbind(dt$V2,dt$V3-dt$V2), file = tmpChrFile, name = chrPos)
+          o <- h5write(obj = cbind(dt$V2,dt$V3 - dt$V2 + 1), file = tmpChrFile, name = chrPos)
           o <- h5write(obj = RG@lengths, file = tmpChrFile, name = chrRGLengths)
           o <- h5write(obj = RG@values, file = tmpChrFile, name = chrRGValues)
 
@@ -1650,7 +1650,7 @@ createArrowFiles <- function(
           o <- .suppressAll(h5createDataset(tmpFile, chrRGValues, storage.mode = "character", 
                     dims = c(lengthRG, 1), level = 0, size = max(nchar(RG@values)) + 1))
 
-          o <- h5write(obj = cbind(dt$start,dt$end-dt$start), file = tmpFile, name = chrPos)
+          o <- h5write(obj = cbind(dt$start, dt$end - dt$start + 1), file = tmpFile, name = chrPos)
           o <- h5write(obj = RG@lengths, file = tmpFile, name = chrRGLengths)
           o <- h5write(obj = RG@values, file = tmpFile, name = chrRGValues)
 
@@ -1686,7 +1686,7 @@ createArrowFiles <- function(
           o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", 
                     dims = c(lengthRG, 1), level = 0, size = max(nchar(RG@values)) + 1))
 
-          o <- h5write(obj = cbind(dt$start,dt$end-dt$start), file = tmpChrFile, name = chrPos)
+          o <- h5write(obj = cbind(dt$start, dt$end - dt$start + 1), file = tmpChrFile, name = chrPos)
           o <- h5write(obj = RG@lengths, file = tmpChrFile, name = chrRGLengths)
           o <- h5write(obj = RG@values, file = tmpChrFile, name = chrRGValues)
 
@@ -1930,14 +1930,29 @@ createArrowFiles <- function(
           chrPos <- paste0("Fragments/",chr,"/Ranges")
           chrRGLengths <- paste0("Fragments/",chr,"/RGLengths")
           chrRGValues <- paste0("Fragments/",chr,"/RGValues")
-          o <- h5createGroup(outArrow, paste0("Fragments/",chr))
-          o <- .suppressAll(h5createDataset(outArrow, chrPos, storage.mode = "integer", dims = c(length(fragments), 2), level = 0))
-          o <- .suppressAll(h5createDataset(outArrow, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
-          o <- .suppressAll(h5createDataset(outArrow, chrRGValues, storage.mode = "character", dims = c(lengthRG, 1), level = 0, 
-                  size = max(nchar(mcols(fragments)$RG@values)) + 1))
-          o <- h5write(obj = cbind(start(fragments),width(fragments)), file = outArrow, name = chrPos)
-          o <- h5write(obj = mcols(fragments)$RG@lengths, file = outArrow, name = chrRGLengths)
-          o <- h5write(obj = mcols(fragments)$RG@values, file = outArrow, name = chrRGValues)
+
+          if(lengthRG == 0){
+          
+            .logMessage(msg = paste0(prefix, " detected 0 Fragments in cells passing filtering threshold for ", chr), logFile = logFile)
+          
+            o <- h5createGroup(outArrow, paste0("Fragments/",chr))
+            o <- .suppressAll(h5createDataset(outArrow, chrPos, storage.mode = "integer", dims = c(0, 2), level = 0))
+            o <- .suppressAll(h5createDataset(outArrow, chrRGLengths, storage.mode = "integer", dims = c(0, 1), level = 0))
+            o <- .suppressAll(h5createDataset(outArrow, chrRGValues, storage.mode = "character", dims = c(0, 1), level = 0, 
+                    size = 10))
+            
+          }else{
+
+            o <- h5createGroup(outArrow, paste0("Fragments/",chr))
+            o <- .suppressAll(h5createDataset(outArrow, chrPos, storage.mode = "integer", dims = c(length(fragments), 2), level = 0))
+            o <- .suppressAll(h5createDataset(outArrow, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
+            o <- .suppressAll(h5createDataset(outArrow, chrRGValues, storage.mode = "character", dims = c(lengthRG, 1), level = 0, 
+                    size = max(nchar(mcols(fragments)$RG@values)) + 1))
+            
+            o <- h5write(obj = cbind(start(fragments),width(fragments)), file = outArrow, name = chrPos)
+            o <- h5write(obj = mcols(fragments)$RG@lengths, file = outArrow, name = chrRGLengths)
+            o <- h5write(obj = mcols(fragments)$RG@values, file = outArrow, name = chrRGValues)
+          }
 
           #Free Some Memory!
           rm(fragments)
@@ -1995,15 +2010,26 @@ createArrowFiles <- function(
           chrRGLengths <- paste0(chr, "._.RGLengths")
           chrRGValues <- paste0(chr, "._.RGValues")
 
-          #HDF5 Write
-          o <- .suppressAll(h5createDataset(tmpChrFile, chrPos, storage.mode = "integer", dims = c(length(fragments), 2), level = 0))
-          o <- .suppressAll(h5createDataset(tmpChrFile, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
-          o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", dims = c(lengthRG, 1), level = 0, 
-                  size = max(nchar(mcols(fragments)$RG@values)) + 1))
-
-          o <- h5write(obj = cbind(start(fragments),width(fragments)), file = tmpChrFile, name = chrPos)
-          o <- h5write(obj = mcols(fragments)$RG@lengths, file = tmpChrFile, name = chrRGLengths)
-          o <- h5write(obj = mcols(fragments)$RG@values, file = tmpChrFile, name = chrRGValues)
+          if(lengthRG == 0){
+                   
+            #HDF5 Write
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrPos, storage.mode = "integer", dims = c(0, 2), level = 0))
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrRGLengths, storage.mode = "integer", dims = c(0, 1), level = 0))
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", dims = c(0, 1), level = 0, 
+                    size = 10))
+
+          }else{
+           
+            #HDF5 Write
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrPos, storage.mode = "integer", dims = c(length(fragments), 2), level = 0))
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrRGLengths, storage.mode = "integer", dims = c(lengthRG, 1), level = 0))
+            o <- .suppressAll(h5createDataset(tmpChrFile, chrRGValues, storage.mode = "character", dims = c(lengthRG, 1), level = 0, 
+                    size = max(nchar(mcols(fragments)$RG@values)) + 1))
+
+            o <- h5write(obj = cbind(start(fragments),width(fragments)), file = tmpChrFile, name = chrPos)
+            o <- h5write(obj = mcols(fragments)$RG@lengths, file = tmpChrFile, name = chrRGLengths)
+            o <- h5write(obj = mcols(fragments)$RG@values, file = tmpChrFile, name = chrRGValues)
+          }
 
           #Free Some Memory!
           rm(fragments)