Using R package ape and cophyloplot to make tanglegram

[SeqTroubles]

Hi All,

I am currently using R to make my phylogenic images Im more familiar with ggtrees and Im not an expert in R in general but can get by.

My aim is to produce a tanglegram of a core and accessory gene data set and colour the association lines based on metadata. I have a file in tab delimited format with this information. It is a rather large phylogeny so inputting colour data for each leaf would be time consuming.

Is there a way colour the association lines using information from separate file to get an end result similar to this

http://www.frontiersin.org/files/Articles/210214/fmicb-07-01581-HTML-r1/image_m/fmicb-07-01581-g006.jpg

Ive tried playing around with the following
cophyloplot(t1, t2, assoc = A1, space=80, length.line=2, show.tip.label = F, col = cols) %<+% info$V3

(cols is a defined set of colours for the metadata Im trying to colour)

cophyloplot help page

https://www.rdocumentation.org/packages/ape/versions/4.1/topics/cophyloplot

Thanks

[SeqTroubles]

Hi All,

I have found this tutorial. https://rpubs.com/tursiops/18942

Which should work but I dont quiet understand how they distinguished and defined the links to be coloured.

[SeqTroubles]

Partially solved

Hi All,

I have found this tutorial. https://rpubs.com/tursiops/18942

Which should work but I dont quiet understand how they distinguished and defined the links to be coloured.

Hi All,

Just in case anyone is interested Ive figured it out, similar to above I extracted the topology order from t1. and merged it without sorting the order with my metadata table. From here I extracted the column of interest as a vector and plugged it into cophyloplot. Please note that x is a numeric vector of genotype data (text vectors would have to be converted from what I can see). See below:

#make association matrix and colour vector
order <- cbind(t1$tip.label)
list <- merge(order, info, by.x="V1", by.y="Samplename", sort=F)
x<- list$Gene
A1 <- cbind(t1$tip.label, t1$tip.label)

#plot tanglegram and colour lines based on associations
cophyloplot(t1,t2, assoc=A1, space=30, length.line=2, show.tip.label = F, col=x)

Now all I need to figure out is how to assign specific colours. Any ideas?