signatureROCplot_CI: Create an array of ROC plots with confidence interval bands...
In TBSignatureProfiler: Profile RA-Seq Data Using TB Pathway Signatures

Description Usage Arguments Value Examples

Create an array of ROC plots with confidence interval bands to compare signatures.

signatureROCplot_CI(
  inputData,
  annotationData,
  signatureColNames,
  annotationColName,
  scale = FALSE,
  choose_colors = c("cornflowerblue", "gray50", "gray79"),
  name = NULL,
  nrow = NULL,
  ncol = NULL,
  ci.lev = 0.95,
  pb.show = TRUE
)

`inputData`	an input data object. It should either be of the class `SummarizedExperiment` and contain the profiled signature data and annotation data as columns in the `colData`, or alternatively be of the classes `data.frame` or `matrix` and contain only the gene expression data. Required.
`annotationData`	a `data.frame` or `matrix` of annotation data, with one column. Only required if `inputData` is a `data.frame` or `matrix` of signature data.
`signatureColNames`	a `vector` of the column names of `inputData` that contain the signature data. If `inputData` is a `SummarizedExperiment` object, these are the column names of the object `colData`.
`annotationColName`	a character string naming the column name in the `colData` that contains the annotation data to be used in making the boxplot. Only required if inputData is a `SummarizedExperiment` object.
`scale`	logical. Setting `scale = TRUE` scales the signature data. The default is `FALSE`.
`choose_colors`	a vector of length 3 defining the colors to be used in the ROC plots. The default is `c("cornflowerblue", "gray50", "gray79")`.
`name`	a character string giving the title of the boxplot. If `NULL`, the plot title will be `"ROC Plots for Gene Signatures, <ci.lev>% Confidence"`. The default is `NULL`.
`nrow`	integer giving the number of rows in the resulting array.
`ncol`	integer giving the number of columns in the resulting array.
`ci.lev`	a number between 0 and 1 giving the desired level of confidence for computing ROC curve estimations.
`pb.show`	logical for whether to show a progress bar while running code. The default is `TRUE`.

An array of ROC plots.

# Run signature profiling

 choose_sigs <- TBsignatures[c(1, 2)]
 prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts",
                                 algorithm = "Zscore",
                                 signatures = choose_sigs,
                                 parallel.sz = 1)

# Create ROC plots with confidence intervals
signatureROCplot_CI(prof_indian, signatureColNames = names(choose_sigs),
                    annotationColName = "label")