pcaplot: Plot a PCA object returned by prcomp

In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Plot a PCA object returned by prcomp

Description

Plot a PCA object returned by prcomp

Usage

pcaplot(
  pca,
  components = 1:2,
  group = NULL,
  col = NULL,
  pch = 19,
  cex = 2,
  legend = NULL,
  ...
)

Arguments

pca	PCA object returned by prcomp
components	a vector of length two indicating the components to plot
group	a factor determining shapes of the points to show (unless overriden by pch=...)
col	Color for plotting (default: internal palette)
pch	Type of character to plot (default: 19)
cex	size of the symbols used for plotting
legend	draw a legend? If legend is a position (eg. "topright"), then a legend is drawn. If NULL or if the group parameter is NULL, then not.
...	any further parameters will be passed to the plot() function (e.g. col, cex, ...)

Details

This is a simplistic function. A much better way is to use the pca2d function from the pca3d package.

Value

If group is NULL, then NULL; else a data frame containing colors and shapes matching each group

tmod documentation built on March 31, 2023, 9 p.m.