plotGeneCount: plotGeneCount

In AUCell: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Description

Plots a histogram and boxplot for the number of genes detected in each cell.

Usage

plotGeneCount(exprMat, plotStats = TRUE, verbose = TRUE)

Arguments

exprMat	Expression matrix (genes as rows, cells as columns)
plotStats	Logical. If true, it plots the histogram, otherwise only calculates the percentages of genes detected.
verbose	Should the function show progress messages? (TRUE / FALSE)

Details

It is important to check that most cells have at least the number of expressed/detected genes that are going to be used to calculate the AUC ('aucMaxRank' in 'calcAUC()'). The histogram provided by 'AUCell_buildRankings()' allows to quickly check this distribution. 'plotGeneCount(exprMatrix)' allows to obtain only the plot before building the rankings.

Value

Quantiles with the number of genes detected by cell (invisible). his result is also printed if verbose=TRUE.

See Also

See the package vignette for more details: vignette("AUCell")

Examples

### (Fake expression matrix)
exprMatrix <- matrix(sample(c(rep(0, 500), sample(1:3, 500, replace=TRUE))),
 nrow=20)
rownames(exprMatrix) <- paste("Gene", 1:20, sep="")
colnames(exprMatrix) <- paste("Sample", 1:50, sep="")
###

plotGeneCount(exprMatrix)
title(sub="Fake expression matrix")

AUCell documentation built on Nov. 8, 2020, 5:51 p.m.