plotScorem {EEM}

Plot score matrix for prcomp result based on group

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"))