AUCell_plotHist: Plot AUC histogram

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

Plot AUC histogram

Description

Plots the distribution of AUC across the cells (for each gene-set) as an histogram.

Usage

AUCell_plotHist(
  cellsAUC,
  aucThr = max(cellsAUC),
  nBreaks = 100,
  onColor = "dodgerblue4",
  offColor = "slategray2",
  ...
)

Arguments

cellsAUC	Subset of the object returned by AUCell_calcAUC (i.e. including only the gene-sets to plot)
aucThr	AUC value planned to use as threshold (to make sure the X axis includes it), if any. Otherwise, the X axis extends to cover only the AUC values plotted.
nBreaks	Number of 'bars' to plot (breaks argument for hist function).
onColor	Color for the bars that pass the AUC threshold
offColor	Color for the bars that do not pass the AUC threshold
...	Other arguments to pass to hist function.

Value

List of histogram objects (invisible).

See Also

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

Examples

# This example is run using a fake expression matrix.
# Therefore, the output will be meaningless.

############# Fake expression matrix #############
set.seed(123)
exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))),
                     nrow=20, 
                     dimnames=list(paste("Gene", 1:20, sep=""), 
                                   paste("Cell", 1:500, sep="")))
dim(exprMatrix)
##################################################

############# Begining of the workflow ###########
# Step 1.
cells_rankings <- AUCell_buildRankings(exprMatrix, plotStats=FALSE)

# Step 2.
# (Gene set: 10 random genes)
genes <- sample(rownames(exprMatrix), 10)
geneSets <- list(geneSet1=genes)
# (aucMaxRank=5 to run with this fake example, it will return 'high' AUC values)
cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5)
##################################################

# Plot histogram:
AUCell_plotHist(cells_AUC["geneSet1",], nBreaks=10)

aertslab/AUCell documentation built on March 12, 2024, 11:40 p.m.