How to colour the branches of an unrooted tree using a variable in R

Question

I would like to generated unrooted neighbour joining trees from input haplotype data, and then colour the branches of the trees based on a variable. I am using the packages Ape and ggtree. The haplotypes and co-variables (metadata) are on two separate files with matching sample names. I have been able to produce trees and colour the tips of the trees by variables, but not the tree branches.

Using mock data -

# Packages
library('ggplot2')
library('ape')
library('phangorn')
library('dplyr')
library('ggtree')
library('phylobase')

# Generate haplotype dataframe
Sample <- c('Sample_A', 'Sample_B', 'Sample_C', 'Sample_D', 'Sample_E', 'Sample_F')
SNP_A <- c(0, 1, 1, 0, 1, 1)
SNP_B <- c(0, 1, 1, 0, 1, 1)
SNP_C <- c(0, 0, 1, 1, 1, 0)
SNP_D <- c(1, 1, 0, 0, 1, 0)
SNP_E <- c(0, 0, 1, 1, 0, 1)
SNP_F <- c(0, 0, 1, 1, 0, 1)
df = data.frame(Sample, SNP_A, SNP_B, SNP_C, SNP_D, SNP_E, SNP_F, row.names=c(1))
df

# Metadata
Factor_A <- c('a', 'a', 'b', 'c', 'a', 'b')
Factor_B <- c('d', 'e', 'd', 'd', 'e', 'd')
df2 = data.frame(Sample, Factor_A, Factor_B)
df2

# Generate Euclidian pairwise distance matrix
pdist = dist(as.matrix(df), method = "euclidean")

# Turn pairwise distance matrix into phylo via neighbour joining method
phylo_nj <- nj(pdist)

I can plot the tree in Ape:

# Example tree plot using Ape
plot(unroot(phylo_nj),
     type="unrooted",
     cex=1,
     use.edge.length=TRUE,
     show.tip.label = TRUE,
     lab4ut="axial",
     edge.width=1.5)

And I can plot the tree in ggtree, adding variables to tip points by colour/ shape:

# Plotting in ggtree
mytree <- ggtree(phylo_nj, layout="equal_angle", size=0.5, linetype=1)
mytree

# Adding metadata variables to tree plot
mytree2 <- mytree %<+% df2 + geom_tippoint(aes(shape = Factor_A,
                                               colour = Factor_B),
                                               size = 9,
                                           alpha=0.7)
mytree2

But I can't work out how to make the branches coloured by a variable (rather than tip points), in either Ape or ggtree. I only want terminal branches coloured, not all of the lines of the tree. My aim is to display two (categorical) variables - one by the branch colour and one by the shape (or colour) of the tip. A crude version of what I'm after would look something like the image below (with Factor_A coded by tip shape (neutral colour as shown) and Factor_B coded by the branch colour.

Thanks in advance for the help.

Answer 1

You can use the function ape::edges after you plot the tree using ape::plot.phylo for colouring specific edges by giving the start/end node making the edge to colour.

## Colouring the first edge with a red dashed line
plot(unroot(phylo_nj), type = "unrooted")
edges(7, 8, col = "red", lty = 2)

Or you can provide a vector of colours directly in the ape::plot.phylo function:

## Making rainbow edges
plot(unroot(phylo_nj), type = "unrooted", edge.color = rainbow(9))

You can find out which edges to colour from your data frame by using the edge table in the phylo object (phylo_nj$edge). For example:

## Which labels have level "a"
labels_a <- df2$Factor_A %in% "a"

## Which edges connect to these labels?
edge_a <- phylo_nj$edge[,2] %in% match(phylo_nj$tip.label, df2$Sample[labels_a])

## Plotting the factors with the labels a coerced as numeric
plot(unroot(phylo_nj), type = "unrooted", edge.color = c("blue", "orange")[edge_a+1])

You can of course expand that to multiple levels by following this method to detect which edge leads to a tip with any factor level.