Produces score plots from pcaBySvd output with the same graphical options as plotScatter as this is a wrapper of this function..
Usage
pcaScorePlot(
resPcaBySvd,
design = NULL,
axes = c(1, 2),
title = "PCA score plot",
points_labs_rn = FALSE,
...
)Arguments
- resPcaBySvd
A list corresponding to the output value of
pcaBySvd.- design
A \(n \times k\) "freely encoded" experimental design data.frame.
- axes
A numerical vector of length 2 with the Principal Components axes to be drawn.
- title
Plot title.
- points_labs_rn
Boolean indicating if the rownames of the scores matrix should be plotted.
- ...
Additional arguments to be passed to
plotScatter.
Details
pcaScorePlot is a wrapper of plotScatter. See ?plotScatter for more information on the additional arguments.
Examples
data("UCH")
# design is explicitly defined
ResPCA <- pcaBySvd(Y = UCH$outcomes)
pcaScorePlot(
resPcaBySvd = ResPCA, axes = c(1, 2),
title = "PCA score plot UCH", design = UCH$design,
color = "Hippurate", shape = "Citrate"
)
# design is recovered from lmpDataList through pcaBySvd()
ResPCA <- pcaBySvd(lmpDataList = UCH)
pcaScorePlot(
resPcaBySvd = ResPCA, axes = c(1, 2),
title = "PCA score plot UCH",
color = "Hippurate", shape = "Citrate"
)
