plot_OneGs_MultSig: Plot ranks of a given gene set across several gene expression...

In fossbert/binilib: Carlo's little helper

Description

This function generates a plot of the member genes of a given gene set across multiple signatures. Its first intention is to illustrate the so called 'percent rank' of a given gene from a given gene set.

Usage

plot_OneGs_MultSig(
  sigmat,
  geneset,
  color = "black",
  signatureNames = NULL,
  gs_label = NULL,
  column_col = NULL,
  scale_alphas = TRUE,
  relative_sigs = FALSE,
  aREA_scores = NULL,
  ...
)

Arguments

sigmat	gene expression matrix, usually of raw values such as read counts, TPM or FPKM
geneset	a character vector representing one gene set
color	single character string indicating a color for the bar lines
signatureNames	Character vector of length 2, specifying the extremes of the signature
gs_label	single character string to label the gene set under investigation
column_col	vector of color ids (character, hex, etc) that must match the number of columns in the signature matrix.
relative_sigs	logical, whether signatures are considered relative, e.g. t-stats or logFC. Will carry out fgsea.
aREA_scores	numeric vector that must match the number of columns from signature matrix, alternative to average rank metric
...	given for compatibility, particularly for the adjustment of cex for various text labels
scale_alpha	logical, whether to scale alpha values for bars, defaults to TRUE

Value

Nothing, a plot is generated in the default output device

Examples

sigmat <- matrix(rnorm(1e5), ncol = 10, nrow = 1e4)
rownames(sigmat) <- paste0('Gene', seq(nrow(sigmat)))
colnames(sigmat) <- paste0('Sample', seq(ncol(sigmat)))
set.seed(42)
gs <- sample(rownames(sigmat), size = 100)
plot_OneGs_MultSig(sigmat = sigmat, geneset = gs)

fossbert/binilib documentation built on April 23, 2021, 10:31 p.m.