plotScorem: Plot score matrix for prcomp result based on group

In chengvt/EEM: Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data

Description

Plot score matrix for prcomp (PCA) result based on group

Usage

plotScorem(prcompResult, ncomp = 4, group, cex = 1.5, col = NULL,
  pch = NULL, legendtitle = NULL, ...)

Arguments

prcompResult	output object from prcomp function
ncomp	maximum number of PC score to plot
group	a vector of numeric, character or factor class separating the samples into groups.
cex	(optional) size of points on graphs
col	point color palette
pch	point type palette
legendtitle	legend title
...	additional arguments to be passed on to pairs

Value

A figure is returned on the graphic device

See Also

pairs, plotScore

Examples

data(applejuice)
# country of apple production
country <- sapply(strsplit(names(applejuice), split = "-"), "[", 1)

applejuice_uf <- unfold(applejuice) # unfold list into matrix
result <- prcomp(applejuice_uf) 
# plot PC1 vs PC3 score based on country of production
plotScorem(result, ncomp = 4, group = country) 

# specify colours
plotScorem(result, ncomp = 4, group = country, col = c("black", "grey"))

chengvt/EEM documentation built on May 13, 2019, 3:51 p.m.