signatureROCplot: Create an array of ROC plots to compare signatures.
In TBSignatureProfiler: Profile RA-Seq Data Using TB Pathway Signatures

Description Usage Arguments Value Examples

Create an array of ROC plots to compare signatures.

signatureROCplot(
  inputData,
  annotationData,
  signatureColNames,
  annotationColName,
  scale = FALSE,
  choose_colors = c("cornflowerblue", "gray24"),
  name = "Signatures",
  nrow = NULL,
  ncol = NULL
)

`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 2 defining the colors to be used in the ROC plots. The default is `c("cornflowerblue", "gray24")`.
`name`	a character string giving the title of the boxplot. The default is `"Signatures"`.
`nrow`	integer giving the number of rows in the resulting array.
`ncol`	integer giving the number of columns in the resulting array.

An array of ROC plots.

# Run signature profiling
 choose_sigs <- subset(TBsignatures,
                       !(names(TBsignatures) %in% c("Lee_4", "Roe_OD_4")))[c(1,2)]
 prof_indian <- runTBsigProfiler(TB_indian, useAssay = "logcounts",
                                 algorithm = "ssGSEA",
                                 signatures = choose_sigs,
                                 parallel.sz = 1)

# Create ROC plots
signatureROCplot(prof_indian, signatureColNames = names(choose_sigs),
                 annotationColName = "label")