node.support: Visualizing Node Support on Phylogenetic Trees
In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description Usage Arguments Note Author(s) See Also Examples

This function plots support values on phylogenetic trees drawn with plot.phylo. Support values above a given cut-off value can be depicted as numbers, colored dots, or thickened branches.

1 2	node.support(x, transfer, cutoff = 0, digits, mode = "numbers", font = 2, pos = "pretty", cex = 0.8, col, legend = FALSE, node, ...)

`x`	A vector of mode `"numeric"` containing node support values.
`transfer`	A list containing the two objects of class `"phylo"`; the first be the source tree, where `x` is taken from, the second being the target tree on which `x` will be plotted.
`cutoff`	A numeric, only support values >= `cutoff` will be considered for plotting.
`digits`	an integer giving the number of digits (see `round`)
`mode`	Either `"numbers"`, `"dots"`, or `"edges"` indicating the way how node support will be plotted (see Examples).
`font`	Fonts to be used for if `mode = "numbers"`: 1 corresponds to plain text (the default), 2 to bold face, 3 to italic, and 4 to bold italic.
`pos`	Position of text if `mode = "numbers"`: `"above"` or `"below"` the subtending edge or to the "right" of the node; if `pos = "pretty"`, text is positioned in a way that tries to minimize touching or intersecting edges.
`cex`	A numeric giving font size, dot size, or thickness of braches depending on the choice of the `mode` argument.
`col`	A character string, giving one or more colors, depending on the choice of the `mode` argument.
`legend`	Logical, if `TRUE` and `mode = "numbers"` a legend is added to the plot.
`node`	A vector of integers giving the number of nodes for which support will displayed; default is all interior nodes.
`...`	Further graphical parameters (from `par`).

node.support requires a previous call of plot.phylo in order to work.

The transfer argument has worked well with example cases I could think of, but has not been tested thoroughly with real data, so be careful and double-check the resulting output.

Natalie Cusimano, modified by Christoph Heibl

plot.phylo, raxml

# phylogenetic tree of wild barley
# --------------------------------
data(hordeum)
hordeum$tip.label <- gsub("H[a-z]+", "H._", hordeum$tip.label)

# plot tree and posterior node support 
# settingchange color, cut-off, and position:
# -------------------------------------------
plot(hordeum)
node.support(hordeum$posterior, cutoff = 0.9, pos = "right",
	col = "red")
	
# you can display up to three support values:
# -------------------------------------------
plot(hordeum)
node.support(hordeum $posterior, cutoff = 0.9, pos = "right",
	col = "red", font = 2)
node.support(hordeum $posterior, cutoff = 0.9, pos = "above",
	col = "blue", font = 1)
node.support(hordeum $posterior, cutoff = 0.9, pos = "below",
	col = "green", font = 3)
	
# the pretty option of the position argument:
# -------------------------------------------
plot(hordeum)
node.support(hordeum $posterior, pos = "pretty")
	
# display support as colored nodes ...
# ...by omitting nodes below threshold
# ------------------------------------
plot(hordeum)
node.support(hordeum $posterior, cutoff = 0.9, mode = "dots",
    col = "black")
# ... or with two colors:
# -----------------------
plot(hordeum)
node.support(hordeum $posterior, cutoff = 0.9, mode = "dots",
    col = c("black", "red"))
    
# display support as bold edges:
# ------------------------------
plot(hordeum)
node.support(hordeum $posterior, cutoff = 0.9, mode = "edges",
    col = "black", cex = 5)	
		
# display support values from a different source tree
# on a target tree:
# -----------------
data(vipera)
# plot maximum likelyhood tree and add 
# bootstrap values from the same tree:
# ------------------------------------
plot(vipera.ml)
node.support(vipera.ml$node.label, pos = "above")
# now transfer posterior probabilities 
# from a Bayesian tree:
# ---------------------
node.support(vipera.bayes$node.label, 
    transfer = list(vipera.bayes, vipera.ml), pos = "below")
    
# this would have been the result without 
# using the transfer argument:
# ----------------------------
node.support(vipera.bayes$node.label, col = "red", pos = "right")