plot_sample_heatmap: Make a heatmap.3 description of the similarity of the genes...

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

Make a heatmap.3 description of the similarity of the genes among samples.

Description

Sometimes you just want to see how the genes of an experiment are related to each other. This can handle that. These heatmap functions should probably be replaced with neatmaps or heatplus or whatever it is, as the annotation dataframes in them are pretty awesome.

Usage

plot_sample_heatmap(
  data,
  colors = NULL,
  design = NULL,
  heatmap_colors = NULL,
  expt_names = NULL,
  dendrogram = "column",
  row_label = NA,
  plot_title = NULL,
  Rowv = TRUE,
  Colv = TRUE,
  label_chars = 10,
  filter = TRUE,
  ...
)

Arguments

data	Expt/expressionset/dataframe set of samples.
colors	Color scheme of the samples (not needed if input is an expt).
design	Design matrix describing the experiment (gotten for free if an expt).
heatmap_colors	Specify a colormap.
expt_names	Alternate samples names.
dendrogram	Where to put dendrograms?
row_label	Passed through to heatmap.2.
plot_title	Title of the plot!
Rowv	Reorder the rows by expression?
Colv	Reorder the columns by expression?
label_chars	Maximum number of characters before abbreviating sample names.
filter	Filter the data before performing this plot?
...	More parameters for a good time!

Value

a recordPlot() heatmap describing the samples.

See Also

[gplots::heatmap.2()]

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