Dev 200402 (GreenleafLab#72)

* bug fix mat column order * force names for getting matrices * force matching cell names * fix * bug fix name order
xuzhougeng · Apr 3, 2020 · e1b8cb6 · e1b8cb6
1 parent 4b50263
commit e1b8cb6
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Showing 3 changed files with 84 additions and 32 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/R/ArrowRead.R b/R/ArrowRead.R
@@ -171,23 +171,37 @@ getMatrixFromProject <- function(
 
   ArrowFiles <- getArrowFiles(ArchRProj)
 
+  cellNames <- ArchRProj$cellNames
+
+
   seL <- ArchR:::.safelapply(seq_along(ArrowFiles), function(x){
 
     .messageDiffTime(paste0("Reading ", useMatrix," : ", names(ArrowFiles)[x], "(",x," of ",length(ArrowFiles),")"), tstart, verbose = verbose)
 
-    o <- getMatrixFromArrow(
-      ArrowFile = ArrowFiles[x],
-      useMatrix = useMatrix,
-      useSeqnames = useSeqnames,
-      cellNames = ArchRProj$cellNames, 
-      ArchRProj = ArchRProj,
-      verbose = verbose,
-      binarize = binarize
-    )
+    allCells <- .availableCells(ArrowFile = ArrowFiles[x], subGroup = useMatrix)
+    allCells <- allCells[allCells %in% cellNames]
+
+    if(length(allCells) != 0){
+
+      o <- getMatrixFromArrow(
+        ArrowFile = ArrowFiles[x],
+        useMatrix = useMatrix,
+        useSeqnames = useSeqnames,
+        cellNames = allCells, 
+        ArchRProj = ArchRProj,
+        verbose = verbose,
+        binarize = binarize
+      )
+
+      .messageDiffTime(paste0("Completed ", useMatrix," : ", names(ArrowFiles)[x], "(",x," of ",length(ArrowFiles),")"), tstart, verbose = verbose)
 
-    .messageDiffTime(paste0("Completed ", useMatrix," : ", names(ArrowFiles)[x], "(",x," of ",length(ArrowFiles),")"), tstart, verbose = verbose)
+      o
+
+    }else{
 
-    o
+      NULL
+
+    }
 
   }, threads = threads) 
 
@@ -281,6 +295,14 @@ getMatrixFromArrow <- function(
   featureDF <- featureDF[BiocGenerics::which(featureDF$seqnames %bcin% seqnames), ]
 
   .messageDiffTime(paste0("Getting ",useMatrix," from ArrowFile : ", basename(ArrowFile)), tstart)
+
+  if(!is.null(cellNames)){
+    allCells <- .availableCells(ArrowFile = ArrowFile, subGroup = useMatrix)
+    if(!all(cellNames %in% allCells)){
+      stop("cellNames must all be within the ArrowFile!!!!")
+    }
+  }
+
   mat <- .getMatFromArrow(
     ArrowFile = ArrowFile, 
     featureDF = featureDF, 
@@ -437,11 +459,14 @@ getMatrixFromArrow <- function(
   mat <- mat[rownames(featureDF), , drop = FALSE]
   rownames(mat) <- NULL
 
+  if(!is.null(cellNames)){
+    mat <- mat[,cellNames,drop=FALSE]
+  }
+
   return(mat)
 
 }
 
-
 ####################################################################
 # Helper read functioning
 ####################################################################
@@ -471,6 +496,16 @@ getMatrixFromArrow <- function(
   rownames(featureDF) <- paste0("f", seq_len(nrow(featureDF)))
   cellNames <- unlist(groupList, use.names = FALSE) ### UNIQUE here? doublet check JJJ
 
+  allCellsList <- lapply(seq_along(ArrowFiles), function(x){
+    allCells <- .availableCells(ArrowFile = ArrowFiles[x], subGroup = useMatrix)
+    allCells <- allCells[allCells %in% cellNames]
+    if(length(allCells) != 0){
+      allCells
+    }else{
+      NULL
+    }
+  })
+
   mat <- .safelapply(seq_along(seqnames), function(x){
 
     .messageDiffTime(sprintf("Constructing Group Matrix %s of %s", x, length(seqnames)), tstart, verbose = verbose)
@@ -484,29 +519,36 @@ getMatrixFromArrow <- function(
     rownames(matChr) <- rownames(featureDFx)
 
     for(y in seq_along(ArrowFiles)){
-
-      maty <- .getMatFromArrow(
-        ArrowFile = ArrowFiles[y], 
-        useMatrix = useMatrix,
-        featureDF = featureDFx, 
-        cellNames = cellNames, 
-        useIndex = useIndex
-      )
 
-      for(z in seq_along(groupList)){
+      allCells <- allCellsList[[y]]
+
+      if(!is.null(allCells)){
+
+        maty <- .getMatFromArrow(
+          ArrowFile = ArrowFiles[y], 
+          useMatrix = useMatrix,
+          featureDF = featureDFx, 
+          cellNames = allCells, 
+          useIndex = useIndex
+        )
 
-        #Check Cells In Group
-        cellsGroupz <- groupList[[z]]
-        idx <- BiocGenerics::which(colnames(maty) %in% cellsGroupz)
+        for(z in seq_along(groupList)){
+
+          #Check Cells In Group
+          cellsGroupz <- groupList[[z]]
+          idx <- BiocGenerics::which(colnames(maty) %in% cellsGroupz)
+
+          #If In Group RowSums
+          if(length(idx) > 0){
+            matChr[,z] <- matChr[,z] + Matrix::rowSums(maty[,idx,drop=FALSE])
+          }
 
-        #If In Group RowSums
-        if(length(idx) > 0){
-          matChr[,z] <- matChr[,z] + Matrix::rowSums(maty[,idx,drop=FALSE])
         }
 
-      }
+        rm(maty)
 
-      rm(maty)
+      }
+
 
       if(y %% 20 == 0 | y %% length(ArrowFiles) == 0){
         gc()
@@ -564,11 +606,22 @@ getMatrixFromArrow <- function(
 
     .messageDiffTime(sprintf("Getting Partial Matrix %s of %s", x, length(ArrowFiles)), tstart, verbose = verbose)
 
+    allCells <- .availableCells(ArrowFile = ArrowFiles[x], subGroup = useMatrix)
+    allCells <- allCells[allCells %in% cellNames]
+
+    if(length(allCells) == 0){
+      if(doSampleCells){
+        return(list(mat = NULL, out = NULL))
+      }else{
+        return(NULL)
+      }
+    }
+
     o <- h5closeAll()
     matx <- .getMatFromArrow(
       ArrowFile = ArrowFiles[x], 
       featureDF = featureDF, 
-      cellNames = cellNames,
+      cellNames = allCells,
       useMatrix = useMatrix, 
       useIndex = useIndex
     )

diff --git a/R/VisualizeData.R b/R/VisualizeData.R
@@ -553,7 +553,7 @@ plotGroups <- function(
 
   if(!inherits(values, "matrix")){
     values <- matrix(as.matrix(values), ncol = nCells(ArchRProj))
-    colnames(values) <- unlist(cellNamesList)
+    colnames(values) <- ArchRProj$cellNames
   }
 
   #Values Summary
@@ -570,7 +570,6 @@ plotGroups <- function(
 
 }
 
-
 .fixPlotSize <- function(
   p = NULL, 
   plotWidth = unit(6, "in"),