Create a Relative Log Expression (RLE) Plot

Generates a Relative Log Expression (RLE) plot for quality assessment of gene expression data. For each feature (row), the median expression across samples is subtracted, and boxplots of the resulting relative expression values are displayed for each sample.

Usage

makeRLEplot(
  E,
  log2.data = TRUE,
  groups = NULL,
  col.group = NULL,
  showTitle = FALSE,
  title = "Relative log expression (RLE) plot",
  ...
)

Arguments

E: A numeric matrix or data frame with features in rows and samples in columns.
log2.data: Logical; if TRUE, expression values are log2-transformed before computing RLE values.
groups: Optional factor or vector defining sample groups. Must have length equal to ncol(E).
col.group: Optional named vector of colours matching group levels.
showTitle: Logical; if TRUE, display a plot title.
title: Character string specifying the plot title.
...: Additional arguments passed to graphics::boxplot().

Value

Invisibly returns the matrix of relative log expression values.

Examples

if (FALSE) { # \dontrun{
set.seed(123)
E <- matrix(rlnorm(987*200, meanlog=5, sdlog=1), nrow=987, ncol=200)
colnames(E) <- paste0("Sample_", seq_len(200))
rownames(E) <- paste0("Gene_", seq_len(987))
group <- rep(c("Control", "Treatment"), each=100)
col.group <- c(Control="steelblue", Treatment="tomato")
par(mar = c(10,4,4,2))
makeRLEplot(E,log2.data=TRUE,groups=group,col.group=col.group,cex=0.4,
  cex.axis=0.5,showTitle=TRUE,title="RLE plot (987 genes×200 samples)")
} # }