plotPathway: Generate violin plots for pathway analysis results

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Generate violin plots for pathway analysis results

Description

Generate violin plots for pathway analysis results

Usage

plotPathway(
  inSCE,
  resultName,
  geneset,
  groupBy = NULL,
  boxplot = FALSE,
  violin = TRUE,
  dots = TRUE,
  summary = "median",
  axisSize = 10,
  axisLabelSize = 10,
  dotSize = 0.5,
  transparency = 1,
  defaultTheme = TRUE,
  gridLine = FALSE,
  title = geneset,
  titleSize = NULL
)

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	Boolean, Whether to add a boxplot. Default FALSE.
violin	Boolean, Whether to add a violin plot. Default TRUE.
dots	Boolean, If TRUE, will plot dots for each violin plot. Default TRUE.
summary	Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median", and NULL for not adding. Default "median".
axisSize	Size of x/y-axis ticks. Default 10.
axisLabelSize	Size of x/y-axis labels. Default 10.
dotSize	Size of dots. Default 0.5.
transparency	Transparency of the dots, values will be 0-1. Default 1.
defaultTheme	Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
gridLine	Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.
title	Title of plot. Default using geneset.
titleSize	Size of the title of the plot. Default 15.

Details

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

Value

A ggplot object for the violin plot

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")
plotPathway(sce, "VAM_GeneSetCollection_CDF", "geneset1")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.