plot_svfactor: Make a dotplot of some categorised factors and a set of SVs...

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

Make a dotplot of some categorised factors and a set of SVs (for other factors).

Description

This should make a quick df of the factors and surrogates and plot them.

Usage

plot_svfactor(
  expt,
  svest,
  sv = 1,
  chosen_factor = "batch",
  factor_type = "factor"
)

Arguments

expt	Experiment from which to acquire the design, counts, etc.
svest	Set of surrogate variable estimations from sva/svg or batch estimates.
sv	Which surrogate to plot?
chosen_factor	Factor to compare against.
factor_type	This may be a factor or range, it is intended to plot a scatterplot if it is a range, a dotplot if a factor.

Value

surrogate variable plot as per Leek's work

See Also

[ggplot2]

Examples

## Not run: 
 estimate_vs_snps <- plot_svfactor(start, surrogate_estimate, "snpcategory")

## End(Not run)

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