Phoebe,
Hi, this was how I solved that problem using plot(). I found using symbols
to be hard to adjust...
#plot the 1st vs 2nd component
plot(x,y,ylab=2nd component, xlab=1st component, xlim=range(x),
ylim=range(y), main=1st vs 2nd component analysis)
#show the arrows, length defined by the 1st and 2nd compoentns
arrows(0,0,ePCAMat$vector[1,]*max(x),ePCAMat$vector[2,]*max(y),length=0.1,
angle=20, col=red)
text(ePCAMat$vector[1,]*max(x)*1.1, ePCAMat$vector[2,]*max(y)*1.1,
names(label), col=red,cex=0.5)
#THIS IS THE PART TO DO THE PLOTTING OF CIRCLES
#You need to calculate the center of each class cluster beforehand
for(i in 1:noClass){
par(new=T)
#specify the center x,y coordinate and then cex = radius
plot(center[i,1],center[i,2],ylab=,
xlab=,xlim=range(x),ylim=range(y),pch=1,cex=mean(distances[i,]),col=(i+1))
}
--
Wai-Kuan YIP
http://www.deakin.edu.au/~waiyip http://www.deakin.edu.au/~waiyip
phoebe kong wrote:
Hi,
I have a hard time in drawing circle on PCA.
I have 60 samples. The corresponding PC1 scores and PC2 scores were stored
as mergedata. Here are the summary of PCs scores.
range(mergedata[,PC1])
[1] 0.0085 0.0100
range(mergedata[,PC2])
[1] 0.0032 0.0075
mean(mergedata[,PC1])
[1] 0.009241667
mean(mergedata[,PC2])
[1] 0.005541667
dim(mergedata)
[1] 60 102
First of all, I need to find the center of the cluster points in PC plot.
Then, I would lilke to draw out from that center concentric circles with
radius 1 SD, 1.5 SD, 2 SD, 2.5 SD and 3 SD.
plot(mergedata[,PC1],mergedata[,PC2],xlab=PC1,ylab=PC2,xlim=range(mergedata[,PC1]),ylim=range(mergedata[,PC2]),pch=20,col=blue)
circle with radius 1SD
symbols(mean(mergedata[,PC1]),mean(mergedata[,PC2]),circle=sd(c(mergedata[,PC2],mergedata[,PC1])),inches=FALSE,add=TRUE)
However, only points were plotted, but the cicle doesn't appear. Could
anyone tell me what's wrong with my code?
Thanks,
Phoebe
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