plot_batchsv: Make a dotplot of known batches vs. SVs.

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

Make a dotplot of known batches vs. SVs.

Description

This should make a quick df of the factors and surrogates and plot them. Maybe it should be folded into plot_svfactor? Hmm, I think first I will write this and see if it is better.

Usage

plot_batchsv(
  expt,
  svs,
  sv = 1,
  batch_column = "batch",
  factor_type = "factor",
  id_column = "sampleid"
)

Arguments

expt	Experiment from which to acquire the design, counts, etc.
svs	Set of surrogate variable estimations from sva/svg or batch estimates.
sv	Which surrogate variable to show?
batch_column	Which experimental design column to use?
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.
id_column	Use this column for the sample IDs.

Value

Plot of batch vs surrogate variables as per Leek's work.

See Also

[sva] [ggplot2]

Examples

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

## End(Not run)

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