rotate2: Swapping Sister Clades
In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description Usage Arguments Details Value Author(s) See Also Examples

This function works exactly in the same manner as rotate in the ape package, but in addition can handle non-standard node label elements like those generated by read.beast.

1	rotate2(phy, node, polytom = c(1, 2))

`phy`	An object of class `"phylo"`.
`node`	A vector of mode numeric or character specifying the number of the node.
`polytom`	A vector of mode numeric and length two specifying the two clades that should be exchanged in a polytomy.

Please refer to rotate.

An object of class "phylo".

Christoph Heibl

read.beast, rotate

# a phylogeny of wild barley
# --------------------------
data(hordeum)
hordeum$tip.label <- LETTERS[1:20]

# rotate phylogeny at node 27
# ---------------------------
node <- 27
hordeum.rotated <- rotate2(hordeum, node)

# plot ...
par(mfcol = c(1, 2), mar = c(0.5, 0.5, 0.5, 0.5))
# ... unmodified tree and 
# -----------------------
plot(hordeum)
nodeInfo(node = node, label = "node to rotate", angle = 160, lex = 8)
node.support(hordeum$posterior, pos = "pretty")


# ... rotated tree
# ----------------
plot(hordeum.rotated, direction = "leftward")
nodeInfo(node = node, label = "rotated node", angle = 340, lex = 6)
node.support(hordeum.rotated$posterior, pos = "pretty")