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I'm trying to create a phylogeny where the branch lengths that I've coded are represented by colour rather than length. So I want the branch lengths to be equal.

Here is my code:

plotBranchbyTrait(tree.scaled, tree.scaled$edge.length, mode=c("edges"),palette="rainbow", use.edge.length = FALSE, node.depth = 2)

It's my understanding that use.edge.length = FALSE should make the branch lengths equal, and it does this if I code the tree using plot.phylo(). But the tree still shows up with the branch lengths when I use plotBranchbyTrait(). Anyone know how to get around this?

mischva11
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Steph Wright
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1 Answers1

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Unfortunately, optional arguments (...) are not directly passed to plot.phylo in the plotBranchbyTrait function. One non-elegant way to fix that is to modify the body directly in R to add a hard coded use.edge.length = FALSE option.

You can do this by creating a new function and modify it using body(foo)[[line_of_interest]] <- substitute(my_new_line <- that_does_something). The following example should work:

## Back up the function
plotBranchbyTrait_no_edge_length <- phytools::plotBranchbyTrait

## The line to modify:
body(plotBranchbyTrait_no_edge_length)[[34]]
# xx <- plot.phylo(tree, type = type, show.tip.label = show.tip.label, 
#    show.node.label = show.node.label, edge.color = colors, edge.width = edge.width, 
#    edge.lty = edge.lty, font = font, cex = cex, adj = adj, srt = srt, 
#    no.margin = no.margin, root.edge = root.edge, label.offset = label.offset, 
#    underscore = underscore, x.lim = x.lim, y.lim = y.lim, direction = direction, 
#    lab4ut = lab4ut, tip.color = tip.color, plot = plot, rotate.tree = rotate.tree, 
#    open.angle = open.angle, lend = 2, new = FALSE)


## Modify the line 34 by adding `use.edge.length = FALSE`
body(plotBranchbyTrait_no_edge_length)[[34]] <- substitute( xx <- plot.phylo(use.edge.length = FALSE, tree, type = type, show.tip.label = show.tip.label, show.node.label = show.node.label, edge.color = colors, edge.width = edge.width,  edge.lty = edge.lty, font = font, cex = cex, adj = adj, srt = srt, no.margin = no.margin, root.edge = root.edge, label.offset = label.offset, underscore = underscore, x.lim = x.lim, y.lim = y.lim, direction = direction, lab4ut = lab4ut, tip.color = tip.color, plot = plot, rotate.tree = rotate.tree, open.angle = open.angle, lend = 2, new = FALSE) )

## Testing whether it worked
library(phytools)
tree <- pbtree(n=50)
x <- fastBM(tree)
## With use.edge.length = TRUE (default)
plotBranchbyTrait(tree, x, mode = "tips", edge.width = 4, prompt = FALSE)

## With use.edge.length = FALSE
plotBranchbyTrait_no_edge_length(tree, x, mode = "tips", edge.width = 4, prompt = FALSE)

You can find more on how to modify functions here.

Thomas Guillerme
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