PCA.PlotScores: Score plot for the results of PCA.Calculate.

In MetStaT: Statistical metabolomics tools

Description

Allows the user to plot a score plot for two or more components. Also allows the user to set advanced labeling options.

Usage

PCA.PlotScores(pr.object, pcs = c(1, 2), labels = "none", custom.labels = NULL, 
dot.class.vector = NULL, col.class.vector = NULL)

Arguments

pr.object	the result of PCA.Calculate
pcs	Which principal components to use for plotting (eg. "1,2" or "1:4")
labels	what type of labels to be used for the scores. Can either be: "none" or "dots" which will plot simple dots, "numerical" which will plot numbers, or "custom" which will plot user defined labels contained in the custom.labels argument.
custom.labels	in case the labels argument is set to "custom", this argument needs to contain a vector of character labels to be used for plotting.
dot.class.vector	NULL by default, in which case all dots are standard dots. A numerical vector can be supplied that defines each dot's symbol type (using R's default number to symbol type conversion).
col.class.vector	NULL by default, in which case all dots are black. A numerical vector can be supplied that defines each dot's color (using R's default number to color conversion).

Value

Only the plot is returned.

Note

When using colors to distinguish between points, keep in mind that only 8 different colors are available. When using symbols to distinguish between points, keep in mind that only 25 different symbols are available.

Author(s)

Tim Dorscheidt

MetStaT documentation built on May 2, 2019, 1:45 p.m.