AUCell_plotHist {AUCell} | R Documentation

## 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)

[Package AUCell version 1.9.8 Index]