Open source software for mass spectrometry and metabolomics - Open Source Software in Life Science Research - page 111

col=as.integer(B),
pch=(as.integer(B)),
cex=3, lwd=3)

col=as.integer(B),
pch=(as.integer(B)),
cex=3, lwd=3)

segments(-plotrangeX, 0, plotrangeX, 0, col='grey')
segments(0, -plotrangeY, 0, plotrangeY, col='grey')

segments(-plotrangeX, 0, plotrangeX, 0, col='grey')
segments(0, -plotrangeY, 0, plotrangeY, col='grey')

text (R$'t1', R$'t2',
labels = substring(rownames(R),1,4),
pos = 4,
offset = 0.5,
cex=1)

text (R$'t1', R$'t2',
labels = substring(rownames(R),1,4),
pos = 4,
offset = 0.5,
cex=1)

To produce the loadings plots, the PCA model is recalculated to obtain
the loadings and R View is used to plot the loadings.

#-------------------------------------------
# PCA Loadings Node (Snippet Node)
#-------------------------------------------
require(pcaMethods)
results=pca(R, method='nipals', centre=FALSE, nPcs=3)
p1=results@loadings[,1]
p2=results@loadings[,2]
p3=results@loadings[,3]
R<-cbind(p1,p2,p3)
R<-R

#-------------------------------------------
# PCA Loadings Node (Snippet Node)
#-------------------------------------------
require(pcaMethods)
results=pca(R, method='nipals', centre=FALSE, nPcs=3)
p1=results@loadings[,1]
p2=results@loadings[,2]
p3=results@loadings[,3]
R<-cbind(p1,p2,p3)
R<-R

#-------------------------------------------
# Loadings Plot (RView Node)
#-------------------------------------------
#calculate axis limits for X
mnX=min(R$'p1')
mxX=max(R$'p1')
plotrangeX=1.2*(max(abs(mnX),abs(mxX))) # add 20%

#-------------------------------------------
# Loadings Plot (RView Node)
#-------------------------------------------
#calculate axis limits for X
mnX=min(R$'p1')
mxX=max(R$'p1')
plotrangeX=1.2*(max(abs(mnX),abs(mxX))) # add 20%

￿ ￿ ￿ ￿ ￿

#calculate axis limits for Y
mnY=min(R$'p2')
mxY=max(R$'p2')
plotrangeY=1.2*(max(abs(mnY),abs(mxY))) # add 20%

#calculate axis limits for Y
mnY=min(R$'p2')
mxY=max(R$'p2')
plotrangeY=1.2*(max(abs(mnY),abs(mxY))) # add 20%

# Plot the loadings
plot(R$p1, R$p2,
main= 'Loadings Plot', sub='First two components',
xlab='p1',
ylab='p2',
xlim = c(-plotrangeX, +plotrangeX),
ylim = c(-plotrangeY, +plotrangeY),
col='red',
pch= 16,
cex=2)

# Plot the loadings
plot(R$p1, R$p2,
main= 'Loadings Plot', sub='First two components',
xlab='p1',
ylab='p2',
xlim = c(-plotrangeX, +plotrangeX),
ylim = c(-plotrangeY, +plotrangeY),
col='red',
pch= 16,
cex=2)