plotDiffPathways: plot pathways enriched in differentially expressed genes

In liuqivandy/scRNABatchQC: a package for quality control of multiple single cell RNAseq data

Description

plot the differentially expressed genes in any pairwise comparison

Usage

plotDiffPathways(
  scesMerge,
  margins = c(5, 5),
  keysize = 1,
  col = colorpanel(75, low = "white", high = "red"),
  ...
)

Arguments

scesMerge	a SingleCellExperiment object; this object contains the combined datasets, pairwise comparison results and reduced dimensions using PCA and tSNE; (results from Combine_scRNAseq)
margins	margins for heatmap.2
keysize	integer for heatmap.2
col	color for heatmap.2
...	parameters passing to heatmap.2

Value

a matrix containing the -log10 FDR of enriched pathways

See Also

Process_scRNAseq, Combine_scRNAseq

Examples

library(scRNABatchQC)
sces<-Process_scRNAseq(inputfile=c("https://github.com/liuqivandy/scRNABatchQC/raw/master/bioplar1.csv.gz",
                                   "https://github.com/liuqivandy/scRNABatchQC/raw/master/bioplar5.csv.gz"))
scesMerge<-Combine_scRNAseq(sces)
plotDiffPathways(scesMerge)

liuqivandy/scRNABatchQC documentation built on March 24, 2021, 11:01 p.m.