Generate violin plots for pathway analysis results

plotPathway(inSCE, resultName, geneset, groupby = NULL, boxplot = FALSE)

Arguments

inSCE	Input SingleCellExperiment object. With `runGSVA()` or `runVAM()` applied in advance.
resultName	A single character of the name of a score matrix, which should be found in `getPathwayResultNames(inSCE)`.
geneset	A single character specifying the geneset of interest. Should be found in the geneSetCollection used for performing the analysis.
groupby	Either a single character specifying a column of `colData(inSCE)` or a vector of equal length as the number of cells. Default `NULL`.
boxplot	Whether to add a boxplot. Default `FALSE`.

Value

A ggplot object for the violin plot

Details

runGSVA() or runVAM() should be applied in advance of using this function. Users can group the data by specifying groupby.

Examples

data("scExample", package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- scaterlogNormCounts(sce, assayName = "logcounts")
gs1 <- rownames(sce)[seq(10)]
gs2 <- rownames(sce)[seq(11,20)]
gs <- list("geneset1" = gs1, "geneset2" = gs2)
sce <- importGeneSetsFromList(inSCE = sce, geneSetList = gs,
                              by = "rownames")
sce <- runVAM(inSCE = sce, geneSetCollectionName = "GeneSetCollection",
              useAssay = "logcounts")
#> Computing VAM distances for 2 gene sets, 195 cells and 200 genes.
#> Min set size: 10, median size: 10
plotPathway(sce, "VAM_GeneSetCollection_CDF", "geneset1")