How do I generate a color-coded tanglegram?

Question

I want to compare two phylogenies and colour the association lines based on some metadata I have. I have been using ape cophyloplot but I have not had any success in getting the lines to colour accurately according to my data (see previous question).

Note that in my actual work flow I define the colour scheme using a palette to control the colour outcome.

I want a means to make a tangle using phylogenies which I can format. Preferably in R. I like to get an output like this:

Answer 1

I think you can try dendextend, in this manual there is an example of coloring the branches. I don't think it is exactly like your coloring, but with a little tweaking you might get your colorscheme in there.

The manual mentions an argument called color_lines for the function tanglegram():

# The `which` parameter allows us to pick the elements in the list to compare
iris_dendlist %>% dendlist(which = c(1,4)) %>% ladderize %>% 
   # untangle(method = "step1side", k_seq = 3:20) %>%
   set("rank_branches") %>%
   tanglegram(common_subtrees_color_branches = TRUE)

According to the manual, the code above produces an image like this:

Try to see if you can fit your color palette in there.

Answer 2

To get your colors in the original order, you can make a dataframe with the labels in the right order with your metadata. You can use merge for this.

So from your example code it would be something like this:

site <- structure(list(name = structure(c(1L, 3L, 4L, 5L, 6L, 7L, 8L,9L, 10L, 2L), .Label = c("t1", "t10", "t2", "t3", "t4", "t5","t6", "t7", "t8", "t9"), class = "factor"), site = c(1L, 1L,1L, 2L, 2L, 3L, 1L, 3L, 2L, 2L)), .Names = c("name", "site"), row.names = c(NA,10L), class = "data.frame") 

library(ape)
library(dendextend)

t1 <- rcoal(10)
t2 <- rcoal(10)

str(site)
# The name are factors now, so make chr first
site$name <- as.character(site$name)

# make a data.frame of your labels
labels_df <- data.frame(t1$tip.label)

#merge the 2 data.frames in the right order (hence sort=F)
colors <- merge(labels_df,site,by.x="t1.tip.label", by.y="name",all.x=T, all.y=F,sort=F)

tanglegram(t1, t2, color_lines=colors$site)

Answer 3

Thanks everyone for the suggestions @b.nota answer is useful to colour according to clade groups but does not address my actual question on using metadata to colour the lines. For this answer see below:

dendextend states for color_lines a vector of colors for the lines connected the labels. If the colors are shorter than the number of labels, they are recycled (and a warning is issued). The colors in the vector are applied on the lines from the bottom up.

# Extract labels from dendrogram on the left
labels <- dendA %>% set("labels_to_char") %>% labels 

#Using a metadata table with colours create a vector of colours
labels <- as.data.frame(labels)
labels2 <- merge(labels, metadata, by.x="labels", by.y="Sample.name", sort=F)
cols <- as.character(labels2$Colours) 

# Make tanglegram
tanglegram(dendA, dendC, color_lines = cols)

Side note if anyone with a phylogeny needs to convert it to a dendrogram to try this on their data see my other question.

Answer 4

As an alternative (though I realise this doesn't really answer the OPs question directly), Dendroscope and Treemap can also produce these types of plots. I don't know if they'll do coloured connections off the top of my head, but I think they can differentially colour the tree branches.

Just in case that is of use!