phylobase (version 0.8.4)

phyloXXYY: Calculate node x and y coordinates

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.

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)

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.

See Also

treePlot, plotOneTree

Examples

# NOT RUN {

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


# }