compareBoxplots: Create a comparison plot of boxplots for bootstrapped AUC...
In TBSignatureProfiler: Profile RA-Seq Data Using TB Pathway Signatures

Description Usage Arguments Value Examples

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

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
)

`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`.

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

# 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)