phylobase (version 0.6.8)

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

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