meanSdPlot: Plot row standard deviations versus row means

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Plot row standard deviations versus row means

Description

This function creates a mean-sd plot for a given SummarizedExperiment object.

Usage

meanSdPlot(
  x,
  ranks = TRUE,
  xlab = ifelse(ranks, "rank(mean)", "mean"),
  ylab = "sd",
  pch,
  plot = TRUE,
  bins = 50,
  ...
)

Arguments

x	A SummarizedExperiment object.
ranks	A logical value indicating whether to plot the rank of the mean instead of the mean.
xlab	A character string for the x-axis label.
ylab	A character string for the y-axis label.
pch	A vector of plotting characters.
plot	A logical value indicating whether to plot the mean-sd plot.
bins	An integer indicating the number of bins in the plot.
...	Other arguments to be passed to the underlying plotting function.

Details

See meanSdPlot for further details

Value

If plot is TRUE, a mean-sd plot is returned. In any case returns a named list with five components: its elements px and py are the x- and y-coordinates of the individual data points in the plot; its first and second element are the x-coordinates and values of the running median estimator (the red line in the plot). Its element gg is the plot object (see examples). Depending on the value of plot, the method can (and by default does) have a side effect, which is to print gg on the active graphics device.

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.