Jim Lemon wrote: >SNN wrote: > > >>Hi, >> >>I have matrix of 300,000*115 (snps*individual). I ran the PCA on the >>covariance matrix which has a dimention oof 115*115. I have the first 100 >>individuals from group A and the rest of 15 individuals from group B. I need >>to plot the data in two and 3 dimentions with respect to PC1 and PC2 and (in >>3D with respect to PC1, PC2 and PC3). I do not know how to have the plot >>ploting the first 100 points corresponding to group A in red (for example) >>and the rest of the 15 points in Blue? i.e I want the each group in a >>diffrent color in the same plot. I appreciate if someone can help. >> >> >> >Hi Nancy, >(if indeed you are a Nancy and that is not a webnym) >Say that your groups really are coded "A" and "B", the group coding >variable is called "group". You can define a color vector like this: > >colorvector<-ifelse(group=="A","red","blue") > >Jim > >______________________________________________ >R-help@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. > > > > Hi Nancy, in your case you may also use inertia ellipses to represent your groups, in addition to different colors. Here is an example using a microsatellite dataset from adegenet (but valid for SNPs of course): ##### library(ade4) library(adegenet) data(microbov) # dataset
# replace missing values obj=na.replace(microbov,method="mean") # perform your pca, keep 3 axes pca1=dudi.pca(obj$tab,scannf=FALSE,nf=3,scale=FALSE) # plot the result s.class(pca1$li,obj$pop) s.class(pca1$li,obj$pop,col=sample(colors(),15)) # here, replace "col" by the appropriate vector of colors. ##### The resulting graphic represents each genotype by a point, and adds ellipses of different color for each group; each ellipse represents 95 % of the inertia of the corresponding group. The more ellipses overlap, the less your groups are differentiated on the factorial plane. Cheers, Thibaut. -- ###################################### Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
