signatureBoxplot {TBSignatureProfiler} | R Documentation

## Plot a boxplot of signature genes.

### Description

Plot a boxplot of signature genes.

### Usage

    signatureBoxplot(
      inputData,
      annotationData,
      signatureColNames,
      annotationColName,
      name = "Signatures",
      scale = FALSE,
      violinPlot = FALSE,
      includePoints = TRUE,
      notch = FALSE,
      rotateLabels = FALSE,
      nrow = NULL,
      ncol = NULL,
      fill_colors = 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 in `colData` that contain the signature data. Only required if `inputData` is a `SummarizedExperiment` object.
`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.
`name` | a character string giving the title of the boxplot. The default is `"Signatures"`.
`scale` | logical. Setting `scale = TRUE` scales the signature data. The default is `FALSE`.
`violinPlot` | logical. Setting `violinPlot = TRUE` creates violin plots in place of boxplots. The default is `FALSE`.
`includePoints` | logical. If `TRUE`, points will be included over the boxplots. The default is `TRUE`.
`notch` | logical. Notches are used to compare groups; if the notches of two boxes do not overlap, this suggests that the medians are significantly different. If `TRUE`, the boxplot will be notched. The default is `FALSE`.
`rotateLabels` | logical. If `TRUE`, the x-axis labels will be rotated. The default is `FALSE`.
`nrow` | integer giving the number of rows in the resulting array.
`ncol` | integer giving the number of columns in the resulting array.
`fill_colors` | a vector of color names to be used as the fill colors for the boxplot. If `NULL`, colors will be supplied via RColorBrewer. The default is `fill_colors = NULL`.

### Value

A `ggplot2` boxplot of the signature data using the provided annotation information.

### Examples

    library(SummarizedExperiment)

    # Generate some artificial data that shows a difference in Zak_RISK_16
    mat_testdata <- rbind(matrix(c(rnorm(80), rnorm(80) + 5), 16, 10,
                                 dimnames = list(TBsignatures$Zak_RISK_16,
                                                 paste0("sample", seq_len(10)))),
                          matrix(rnorm(1000), 100, 10,
                                 dimnames = list(paste0("gene", seq_len(100)),
                                                 paste0("sample", seq_len(10)))))

    # Create a SummarizedExperiment object that contains the data
    testdataSE <- SummarizedExperiment(assays = SimpleList(data = mat_testdata),
                                       colData = DataFrame(sample =
                                                             c(rep("down", 5),
                                                               rep("up", 5))))

    # Run profiler using GSVA and ssGSEA on Zak_RISK_16 signature
    res <- runTBsigProfiler(testdataSE, useAssay = "data",
                            signatures = TBsignatures["Zak_RISK_16"],
                            algorithm = c("GSVA", "ssGSEA"), parallel.sz = 1,
                            combineSigAndAlgorithm = TRUE)
    signatureBoxplot(res, signatureColNames = c("GSVA_Zak_RISK_16",
                                                "ssGSEA_Zak_RISK_16"),
                     annotationColName = "sample", name = "Zak_RISK_16 Signature")

[Package TBSignatureProfiler version 1.4.11 Index]