Merge pull request #757 from joshua-d-campbell/devel

more GSVA fixes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: singleCellTK
 Type: Package
 Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
-Version: 2.13.2
+Version: 2.13.3
 Authors@R: c(person(given="Yichen", family="Wang", email="[email protected]", role=c("aut"),
                     comment = c(ORCID = "0000-0003-4347-5199")),
              person(given="Irzam", family="Sarfraz", email="[email protected]", role=c("aut"),
@@ -62,7 +62,7 @@ Imports:
     ggrepel,
     ggtree,
     gridExtra,
-    GSVA (>= 1.26.0),
+    GSVA (>= 1.50.0),
     GSVAdata,
     igraph,
     KernSmooth,

R/runGSVA.R

@@ -35,7 +35,7 @@ runGSVA <- function(inSCE, useAssay = "logcounts",
 
   message(date(), " ... Running GSVA")
 
-  gsvaData <- as.matrix(expData(sce, useAssay))
+  gsvaData <- as.matrix(expData(inSCE, useAssay))
   gsvaPar <- GSVA::gsvaParam(gsvaData, gene.Set)
   gsvaRes <- t(GSVA::gsva(gsvaPar))
 

tests/testthat/test-pathway.R

@@ -33,7 +33,7 @@ test_that(desc = "Testing VAM", {
 })
 
 test_that(desc = "Testing GSVA", {
-    sce <- runGSVA(sce, geneSetCollectionName = "GeneSetCollection")
+    sce <- runGSVA(sce, geneSetCollectionName = "GeneSetCollection", useAssay = "logcounts")
     testthat::expect_true("GSVA_GeneSetCollection_Scores" %in% reducedDimNames(sce))
 
     gsvaPlot <- plotPathway(sce, resultName = "GSVA_GeneSetCollection_Scores",