phylogeny

I am trying to create circular phylogenetic tree. I have this part of code: fit<- hclust(dist(Data[,-4]), method = "complete", members = NULL) nclus= 3 color=c('red','blue','green') color_list=rep(color,nclus/length(color)) clus=cutree(fit,nclus) plot(as.phylo(fit),type='fan',tip.color=color_list[clus],label.offset=0.2,no.margin=TRUE, cex=0.70, show.node.label = TRUE) And this is result: Also I am trying to show label for each node and to color branches. Any suggestion how to do that? Thanks! When you say "color branches" I assume you mean color the edges. This seems to work, but I have to

Following a previous post ( Label and color leaf dendrogram in r ) I have a follow-up question. My questions are similar to the post mentioned but I wonder can it be done using ape (e.g., plot(as.phylo(fit), type="fan", labelCol) as it has more type of phylogeny. The mentioned post questions were: How can I show the group codes in leaf label (instead of the sample number)? I wish to assign a color to each code group and colored the leaf label according to it (it might happen that they will not be in the same clade and by that I can find more information)? And the code sample is: sample = data

I know dendrograms are quite popular. However if there are quite large number of observations and classes it hard to follow. However sometime I feel that there should be better way to present the same thing. I got an idea but do not know how to implement it. Consider the following dendrogram. > data(mtcars) > plot(hclust(dist(mtcars))) Can plot it like a scatter plot. In which the distance between two points is plotted with line, while sperate clusters (assumed threshold) are colored and circle size is determined by value of some variable. You are describing a fairly typical way of going about

In a phylogenetic fan, I would like to colour code the tips (resembling 62 species in this example) by applying an if-statement. I am currently using the following code, in an attempt to colour all species associated with "O" darkgreen: ColourIf = ifelse(LU != "O", "blue", "darkgreen") tiff("PhyloFan.tif", height=10, width=10, units="in", res=300, compression="lzw"); plot.phylo(phyloFan,type="fan",show.tip.label=T,cex=0.9,show.node.label=F, edge.color="black", adj=0, label.offset=0.75, lwd=2, edge.width=1, tip.color=ColourIf) par(oma=c(0,0,0,0)) dev.off() At the moment, seven species are

When using the haploNet package to make some plots on a haplotype network, I used a script available on the internet to do so. However I think there is something wrong. The script is available in form of the woodmouse example. The code I used is: x <- read.dna(file="Masto.fasta",format="fasta") h <- haplotype(x) net <- haploNet(h) plot(net) plot(net, size = attr(net, "freq"), fast = TRUE) plot(net, size = attr(net, "freq")) plot(net, size=attr(net, "freq"), scale.ratio = 2, cex = 0.8 table(rownames(x)) ind.hap<-with( stack(setNames(attr(h, "index"), rownames(h))), table(hap=ind, pop=rownames(x