compareBoxplots {TBSignatureProfiler} | R Documentation

## Create a comparison plot of boxplots for bootstrapped AUC values.

### Description

Present the results of AUC bootstrapping for a collection of scored signatures via boxplots.

### Usage

    compareBoxplots(
      SE_scored,
      annotationColName,
      signatureColNames,
      num.boot = 100,
      name = "Boxplot Comparison of Signature AUCs",
      pb.show = TRUE,
      abline.col = "red",
      fill.col = "gray79",
      outline.col = "black",
      rotateLabels = FALSE,
      violinPlot = FALSE
    )

### Arguments

`SE_scored` | a `SummarizedExperiment` object with genes as the row features and signature scores in the `colData`. There should also be a column of annotation data. Required.
`annotationColName` | a character string giving the column name in `colData` that contains the annotation data. Required.
`signatureColNames` | a vector of column names in the `colData` that contain the signature score data. Required.
`num.boot` | an integer indicating the number of times to bootstrap the data.
`name` | a character string giving the overall title for the plot. The default is `"Boxplot Comparison of Signature AUCs"`.
`pb.show` | logical for whether to show a progress bar while running code. Default is `TRUE`.
`abline.col` | the color to be used for the dotted line at AUC = 0.5 (the chance line). The default is `"red"`.
`fill.col` | the color to be used to fill the boxplots. The default is `"white"`.
`outline.col` | the color to be used for the boxplot outlines. The default is `"black"`.
`rotateLabels` | If `TRUE`, rotate labels. Default is `FALSE`.
`violinPlot` | logical. Setting `violinPlot = TRUE` creates violin plots in place of boxplots. The mean and +/- 1 standard deviation are added to the violin plot interior for each signature. The default is `FALSE`.

### Value

A plot with side-by-side boxplots of bootstrapped AUC values for each specified signature.

### Examples

    # Run signature profiling
     choose_sigs <- TBsignatures[c(1, 2)]
     prof_indian <- runTBsigProfiler(TB_indian[seq_len(25), ],
                                     useAssay = "logcounts",
                                     algorithm = "ssGSEA",
                                     signatures = choose_sigs,
                                     parallel.sz = 1)
     # Create boxplots
     compareBoxplots(prof_indian, annotationColName = "label",
                     signatureColNames = names(choose_sigs), rotateLabels = TRUE)

[Package TBSignatureProfiler version 1.4.11 Index]