signatureBoxplot: Plot a boxplot of signature genes.
In TBSignatureProfiler: Profile RA-Seq Data Using TB Pathway Signatures

Description Usage Arguments Value Examples

Plot a boxplot of signature genes.

signatureBoxplot(
  inputData,
  annotationData,
  signatureColNames,
  annotationColName,
  name = "Signatures",
  scale = FALSE,
  includePoints = TRUE,
  notch = FALSE,
  rotateLabels = FALSE,
  nrow = NULL,
  ncol = NULL,
  fill_colors = 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 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`.
`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`.

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

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")