Hello, I am facing problem in plotting an unrooted neighbor joining tree based on hamming distance. I have got a figure of my tree. But the labels are overlapped with each other. I used cex=0.5 but it only reduced the font size of my labels but still the problem persist. I used the following codes:
hamdist<- dist.dna(snpdata, model="N") tree_nj <- nj(hamdist) plot.phylo(tree_nj, type="unrooted", lab4ut=c("horizontal"),no.margin=T, cex=0.5 ) par(mfrow=c(1,1))
I could not attach the figure.
Another problem is with the principal component analysis in R. My data contains 250 locus of 100 individuals. And the SNP data is simulated so I do not have any population name or class or information. I am trying to use "s.class" for plotting the figure of PCA. But every time there is this error message "
Error in s.class(PGRtp_ID8_pca$li, seq2$pop, lab = seq2$pop.names) : factor expected for fac".
Now please tell me is there any other method to other than s.class for plotting PCA and get a good figure? Or how can i plot the figure with s.class?
Please also tell me how can I solve the problem with my phylogenetic tree.