plot_corheat: Make a heatmap.3 description of the correlation between...

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

Make a heatmap.3 description of the correlation between samples.

Description

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

Usage

plot_corheat(
  expt_data,
  expt_colors = NULL,
  expt_design = NULL,
  method = "pearson",
  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 for the samples, not needed if this is an expt.
expt_design	Design matrix describing the experiment, not needed if this is an expt.
method	Correlation statistic to use. (pearson, spearman, kendall, robust).
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 options are wonderful!

Value

Gplots heatmap describing describing how the samples are clustering vis a vis pairwise correlation.

See Also

[grDevice] [gplot2::heatmap.2()]

Examples

## Not run: 
 corheat_plot <- hpgl_corheat(expt = expt, method = "robust")

## End(Not run)

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