Merge pull request #755 from mingl1997/devel

Fixes for BioC release
compbiomed · Apr 16, 2024 · 602b646 · 602b646
2 parents a78fbac + 7273626
commit 602b646
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Showing 4 changed files with 29 additions and 13 deletions.
diff --git a/R/getTopHVG.R b/R/getTopHVG.R
@@ -98,6 +98,10 @@ getTopHVG <- function(inSCE,
         geneIdx <- featureIndex(topGenes, inSCE)
         topGenes <- rowData(inSCE)[[featureDisplay]][geneIdx]
     }
+
+    topGenes <- topGenes[!is.na(topGenes)]
+    topGenes <- topGenes[1:hvgNumber]
+
     return(topGenes)
 }
 

diff --git a/R/seuratFunctions.R b/R/seuratFunctions.R
@@ -2045,6 +2045,8 @@ runSeuratFindMarkers <- function(inSCE,
 #' @param features Specify the features to compute the plot against.
 #' @param groupVariable Specify the column name from the colData slot that
 #' should be used as grouping variable.
+#' @param reducedDimName Specify the name of the dimensional reduction to be used. 
+#' Default is "seuratNormData".
 #' @param splitBy Specify the column name from the colData slot that should be
 #' used to split samples.
 #'  Default is \code{NULL}.

diff --git a/exec/SCTK_runQC.R b/exec/SCTK_runQC.R
@@ -246,7 +246,7 @@ if (is.null(subTitles)) {
 
 if ("HTAN" %in% formats) {
     if (!("FlatFile" %in% formats)) {
-        message("Notice: HTAN specified as output without FlatFile. Automatically including FlatFile export.")
+        message("Note: HTAN specified as output without FlatFile. Automatically including FlatFile export.")
         formats <- append(formats, "FlatFile")
     }
 }
@@ -334,18 +334,26 @@ if (!is.null(gmt)) {
 level3Meta <- list()
 level4Meta <- list()
 
-if (!is.null(flatFiles)) {
-    flatFiles <- split(flatFiles, ceiling(seq_along(flatFiles)/6))
-}
-
 for(i in seq_along(process)) {
+
+    # pop elements from FlatFile input list
+    if ("FlatFile" %in% process[i]) {
+        if (dataType %in% c("Droplet", "Cell")) {
+            flatFileInput <- flatFiles[c(1, 2, 3)]
+            flatFiles <- flatFiles[-c(1, 2, 3)]
+        }
+        else {
+            flatFileInput <- flatFiles[c(1, 2, 3, 4, 5, 6)]
+            flatFiles <- flatFiles[-c(1, 2, 3, 4, 5, 6)]
+        }
+    }
+
     preproc <- process[i]
     samplename <- sample[i]
     path <- basepath[i]
     raw <- RawDir[i]
     fil <- FilterDir[i]
     ref <- Reference[i]
-    flatFiles <- flatFiles[[i]]
     rawFile <- RawFile[i]
     filFile <- FilterFile[i]
     subTitle <- subTitles[i]
@@ -357,7 +365,7 @@ for(i in seq_along(process)) {
                             ref,
                             rawFile,
                             filFile,
-                            flatFiles,
+                            flatFileInput,
                             dataType)
     dropletSCE <- INPUT[[1]]
     cellSCE <- INPUT[[2]]
@@ -366,6 +374,7 @@ for(i in seq_along(process)) {
 
     cellQCAlgos <- c("QCMetrics", "scDblFinder", "cxds", "bcds", "scrublet", "doubletFinder",
     "cxds_bcds_hybrid", "decontX", "decontX_bg", "soupX", "soupX_bg") #scrublet
+
 
     # Checking to see if the input is a file instead of a directory, for RDS and H5AD reading
     # also check to see if the sample name is specified, and if so, set it

diff --git a/tests/testthat/test-featureSelection.R b/tests/testthat/test-featureSelection.R
@@ -23,12 +23,13 @@ test_that(desc = "Testing FindHVG", {
     testthat::expect_true(all(metricNames.mvp %in% names(rowData(sce))))
 
     # Test accessor functions
-    sce <- setTopHVG(sce, "modelGeneVar", hvgNumber = 2000, altExp = TRUE, featureSubsetName = NULL)
-    nHVG <- length(getTopHVG(sce, useFeatureSubset = "HVG_modelGeneVar2000"))
+    sce <- setTopHVG(sce, "modelGeneVar", hvgNumber = 50, altExp = TRUE, featureSubsetName = NULL)
+    #sce <- setTopHVG(sce, "modelGeneVar", hvgNumber = 2000, altExp = TRUE, featureSubsetName = NULL)
+    nHVG <- length(getTopHVG(sce, hvgNumber = 50, useFeatureSubset = "HVG_modelGeneVar50"))
 
-    testthat::expect_true(is.logical(rowData(sce)$HVG_modelGeneVar2000))
-    testthat::expect_equal(nrow(altExp(sce, "HVG_modelGeneVar2000")), nHVG)
-    testthat::expect_equal(metadata(sce)$sctk$featureSubsets$HVG_modelGeneVar2000$useAssay,
+    testthat::expect_true(is.logical(rowData(sce)$HVG_modelGeneVar50))
+    testthat::expect_equal(nrow(altExp(sce, "HVG_modelGeneVar50")), nHVG)
+    testthat::expect_equal(metadata(sce)$sctk$featureSubsets$HVG_modelGeneVar50$useAssay,
                            "seuratNormData")
 
     hvgs <- getTopHVG(sce, "mean.var.plot", hvgNumber = 2000,
@@ -39,7 +40,7 @@ test_that(desc = "Testing FindHVG", {
     vm2 <- plotTopHVG(sce, "modelGeneVar", hvgNumber = 30, labelsCount = 10,
                      featureDisplay = "feature_name")
     vm3 <- plotTopHVG(sce, method = "mean.var.plot",
-                      useFeatureSubset = "HVG_modelGeneVar2000", hvgNumber = NULL)
+                      useFeatureSubset = "HVG_modelGeneVar50", hvgNumber = NULL)
     testthat::expect_true(inherits(vm1, "ggplot"))
     testthat::expect_true(inherits(vm2, "ggplot"))
     testthat::expect_true(inherits(vm3, "ggplot"))