Question

我正在尝试创建系统发育树，其中我编码的分支长度由颜色而不是长度表示。所以我希望分支长度相等。

这是我的代码：

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

据我了解，use.edge.length = FALSE应该使分支长度相等，如果我使用plot.phylo()对树进行编码，就可以做到这一点。但是当我使用plotBranchbyTrait()时，树仍然显示出分支长度。有人知道如何解决这个问题吗？

Answer 1

不幸的是，可选参数(...)在plot.phylo函数中没有直接传递给plotBranchbyTrait。一种非优雅的修复方法是直接在R中修改主体以添加硬编码的use.edge.length = FALSE选项。

您可以通过创建一个新功能并使用body(foo)[[line_of_interest]] <- substitute(my_new_line <- that_does_something)对其进行修改来做到这一点。以下示例应该起作用：

## 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)

您可以找到有关如何修改功能here的更多信息。

在phytools中使用plotBranchbyTrait（）时，“ use.edge.length = FALSE”似乎不起作用

1 个答案: