plotPCPathways: plot pathways enriched in PC-related genes

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

Description

plot the pathways enriched in the PC genes across single cell RNAseq datasets

Usage

plotPCPathways(
  sces,
  margins = c(5, 10),
  keysize = 1,
  col = colorpanel(75, low = "white", high = "red"),
  ...
)

Arguments

sces	list; a list of SingleCellExperiment objects; each object containing QC metadata for each dataset; (results from Process_scRNAseq )
margins	margins for heatmap.2 (default: c(5,10))
keysize	integer for heatmap.2 (default: 1)
col	color for heatmap.2 (default: colorpanel(75,low="white",high="red"))
...	parameters passing to heatmap.2

Value

a matrix containing the -log10 FDR of enriched pathways in each dataset

See Also

Process_scRNAseq

Examples

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

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