plotQuantitative {TBSignatureProfiler} | R Documentation

## Create a boxplot using logistic regression and bootstrap LOOCV to evaluate signatures.

### Description

This function takes as input a `data.frame` with genetic expression count data, and uses a bootstrapped leave-one-out cross validation procedure with logistic regression to allow for numeric and graphical comparison across any number of genetic signatures. It creates a boxplot of bootstrapped AUC values.

### Usage

    plotQuantitative(
      df.input,
      targetVec.num,
      signature.list = NULL,
      signature.name.vec = NULL,
      num.boot = 100,
      pb.show = TRUE,
      name = "Signature Evaluation: Bootstrapped AUCs",
      fill.col = "white",
      outline.col = "black",
      abline.col = "red",
      rotateLabels = FALSE
    )

### Arguments

`df.input` | a `data.frame` of gene expression count data. Required.
`targetVec.num` | a numeric binary vector of the response variable. The vector should be the same number of rows as `df`. Required.
`signature.list` | a `list` of signatures to run with their associated genes. This list should be in the same format as `TBsignatures`, included in the TBSignatureProfiler package. If `signature.list = NULL`, the default set of signatures `TBsignatures` list is used. For details, run `?TBsignatures`.
`signature.name.vec` | A vector specifying the names of the signatures to be compared. This should be the same length as `signature.list`. If `signature.name.vec = NULL`, the default set of signatures `TBsignatures` list is used.
`num.boot` | an integer specifying the number of bootstrap iterations.
`pb.show` | logical. If `TRUE` then a progress bar for the bootstrapping procedure will be displayed as output. The default is `TRUE`.
`name` | a character string giving a name for the outputted boxplot of bootstrapped AUCs. The default is `"Signature Evaluation: Bootstrapped AUCs"`.
`fill.col` | the color to be used to fill the boxplots. The default is `"white"`.
`outline.col` | the color to be used for the boxplot outlines. The default is `"black"`.
`abline.col` | the color to be used for the dotted line at AUC = 0.5 (the chance line). The default is `"red"`.
`rotateLabels` | logical. If `TRUE`, the x-axis labels will be rotated. The default is `FALSE`.

### Value

a boxplot comparing the bootstrapped AUCs of inputted signatures

### Examples

    inputTest <- matrix(rnorm(1000), 100, 20,
                        dimnames = list(paste0("gene", seq.int(1, 100)),
                                        paste0("sample", seq.int(1, 20))))
    inputTest <- as.data.frame(inputTest)
    targetVec <- sample(c(0,1), replace = TRUE, size = 20)
    signature.list <- list(sig1 = c("gene1", "gene2", "gene3"),
                           sig2 = c("gene4", "gene5", "gene6"))
    signature.name.vec <- c("sig1", "sig2")
    num.boot <- 5
    plotQuantitative(inputTest, targetVec.num = targetVec,
                     signature.list = signature.list,
                     signature.name.vec = signature.name.vec,
                     num.boot = num.boot, rotateLabels = FALSE)

[Package TBSignatureProfiler version 1.6.0 Index]