phyloXXYY: Calculate node x and y coordinates

In phylobase: Base package for phylogenetic structures and comparative data

Description

Calculates the node x and y locations for plotting a phylogenetic tree.

Usage

phyloXXYY(phy, tip.order = NULL)

Arguments

phy	A phylo4 or phylo4d object.
tip.order	A character vector of tip labels, indicating their order along the y axis (from top to bottom). Or, a numeric vector of tip node IDs indicating the order.

Details

The y coordinates of the tips are evenly spaced from 0 to 1 in pruningwise order. Ancestor y nodes are given the mean value of immediate descendants. The root is given the x coordinate 0 and descendant nodes are placed according to the cumulative branch length from the root, with a maximum x value of 1.

Value

yy	Internal node and tip y coordinates
xx	Internal node and tip x coordinates
phy	A phylo4 or phylo4d object
segs	A list of h0x, h1x, v0x, v1x and h0y, h1y, v0y, v1y describing the start and end points for the plot line segments
torder	The tip order provided as tip.order or if NULL the preoder tip order
eorder	The an index of the reordered edges compared to the result of edges(phy)

Author(s)

Peter Cowan [e-mail]

See Also

treePlot, plotOneTree

Examples

data(geospiza)
coor <- phyloXXYY(geospiza)
plot(coor$xx, coor$yy, pch = 20)

Example output

phylobase documentation built on May 2, 2019, 6:49 p.m.