plot_variance_coefficients: Look at the (biological)coefficient of variation/quartile...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Look at the (biological)coefficient of variation/quartile coefficient of dispersion with respect to an experimental factor.

Description

I want to look at the (B)CV of some data with respect to condition/batch/whatever. This function should make that possible, with some important caveats. The most appropriate metric is actually the biological coefficient of variation as calculated by DESeq2/EdgeR; but the metrics I am currently taking are the simpler and less appropriate CV(sd/mean) and QCD(q3-q1/q3+q1).

Usage

plot_variance_coefficients(
  data,
  design = NULL,
  x_axis = "condition",
  colors = NULL,
  plot_title = NULL,
  ...
)

Arguments

data	Expressionset/epxt to poke at.
design	Specify metadata if necessary.
x_axis	Factor in the experimental design we may use to group the data and calculate the dispersion metrics.
colors	Set of colors to use when making the violins
plot_title	Optional title to include with the plot.
...	Extra arguments to pass along.

Value

List of plots showing the coefficients vs. genes along with the data.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.