signatureROCplot {TBSignatureProfiler} | R Documentation

## Create an array of ROC plots to compare signatures.

### Description

Create an array of ROC plots to compare signatures.

### Usage

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

### Arguments

`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.

### Value

An array of ROC plots.

### Examples

    # 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")

[Package TBSignatureProfiler version 1.4.11 Index]