setwd("/Users/apple/Desktop/R/")
data<-read.table("pcadata",header=T,row.names=1)
PCAdata.pr<-princomp(data,cor=TRUE)
summary(PCAdata.pr,loadings=TRUE)
predict(PCAdata.pr)
screeplot(PCAdata.pr,type="lines")
biplot(PCAdata.pr,choices=1:2,scale=1,pc.biplot=FALSE)
scoresdata=PCAdata.pr$scores
scoredatasz<-read.table("scoredatasz.txt",header=T,row.names=1)
library(scatterplot3d)
> with(scoredatasz, {
s3d <- scatterplot3d(Comp.1, Comp.2, Comp.3, # x y and z axis
pch=19, # circle color indicates no. of cylinders
scale.y=.75, # scale y axis (reduce by 25%)
main="PCA analysis",
xlab="PCA1(47.12%)",
ylab="PCA2(16.65%)",
zlab="PCA3(16.03%)")
s3d.coords <- s3d$xyz.convert(Comp.1, Comp.2, Comp.3)
text(s3d.coords$x, s3d.coords$y, # x and y coordinates
labels=row.names(scoredatasz), # text to plot
pos=4, cex=.5) # shrink text 50% and place to right of points)
})
loaddatasz<-read.table("loadsz.txt",header=T,row.names=1)
with(loaddatasz, {
s3d <- scatterplot3d(Comp.1, Comp.2, Comp.3, # x y and z axis
pch=19, # circle color indicates no. of cylinders
scale.y=.75, # scale y axis (reduce by 25%)
main="PCA analysis",
xlab="PCA1(32.44%)",
ylab="PCA2(22.94%)",
zlab="PCA3(12.83%)")
s3d.coords <- s3d$xyz.convert(Comp.1, Comp.2, Comp.3)
text(s3d.coords$x, s3d.coords$y, # x and y coordinates
labels=row.names(loaddatasz), # text to plot
pos=4, cex=.5) # shrink text 50% and place to right of points)
})
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