plot_disheat: Make a heatmap.3 of the distances (euclidean by default)...

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

Make a heatmap.3 of the distances (euclidean by default) between samples.

Description

Given a set of count tables and design, this will calculate the pairwise distances and plot them as a heatmap. It attempts to standardize the inputs and eventual output.

Usage

plot_disheat(
  expt_data,
  expt_colors = NULL,
  expt_design = NULL,
  method = "euclidean",
  expt_names = NULL,
  batch_row = "batch",
  plot_title = NULL,
  label_chars = 10,
  ...
)

Arguments

expt_data	Dataframe, expt, or expressionset to work with.
expt_colors	Color scheme (not needed if an expt is provided).
expt_design	Design matrix (not needed if an expt is provided).
method	Distance metric to use.
expt_names	Alternate names to use for the samples.
batch_row	Name of the design row used for 'batch' column colors.
plot_title	Title for the plot.
label_chars	Limit on the number of label characters.
...	More parameters!

Value

a recordPlot() heatmap describing the distance between samples.

See Also

[gplots::heatmap.2()]

Examples

## Not run: 
 disheat_plot = plot_disheat(expt = expt, method = "euclidean")

## End(Not run)

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