plot_heatmap: Make a heatmap.3 plot, does the work for plot_disheat and...

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

Make a heatmap.3 plot, does the work for plot_disheat and plot_corheat.

Description

This does what is says on the tin. Sets the colors for correlation or distance heatmaps, handles the calculation of the relevant metrics, and plots the heatmap.

Usage

plot_heatmap(
  expt_data,
  expt_colors = NULL,
  expt_design = NULL,
  method = "pearson",
  expt_names = NULL,
  type = "correlation",
  batch_row = "batch",
  plot_title = NULL,
  label_chars = 10,
  ...
)

Arguments

expt_data	Dataframe, expt, or expressionset to work with.
expt_colors	Color scheme for the samples.
expt_design	Design matrix describing the experiment vis a vis conditions and batches.
method	Distance or correlation metric to use.
expt_names	Alternate names to use for the samples.
type	Defines the use of correlation, distance, or sample heatmap.
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.
...	I like elipses!

Value

a recordPlot() heatmap describing the distance between samples.

See Also

[gplots::heatmap.2()]

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