plotGeneCount {AUCell} | R Documentation

## plotGeneCount

### 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")

[Package AUCell version 1.8.0 Index]