The ade4 Package - NexTag Supports Open Source Initiatives

plot.phylog 203
f.phylog
circle
cleaves
cnodes
a size coefficient for tree size (a parameter to draw the tree in proportion to
leaves label)
a size coefficient for the outer circle
a character size for plotting the points that represent the leaves, used with par("cex")*cleaves.
If zero, no points are drawn
a character size for plotting the points that represent the nodes, used with par("cex")*cnodes.
If zero, no points are drawn
labels.leaves
a vector of strings of characters for the leaves labels
clabel.leaves
a character size for the leaves labels, used with par("cex")*clabel.leaves.
If zero, no leaves labels are drawn
labels.nodes a vector of strings of characters for the nodes labels
clabel.nodes a character size for the nodes labels, used with par("cex")*clabel.nodes.
If zero, no nodes labels are drawn
sub
csub
possub
draw.box
a string of characters to be inserted as legend
a character size for the legend, used with par("cex")*csub
a string of characters indicating the sub-title position ("topleft", "topright", "bottomleft",
"bottomright")
if TRUE draws a box around the current plot with the function box()
... further arguments passed to or from other methods
no.over
a size coefficient for the number of representations
Details
The vector y is an argument of the function plot.phylog that ensures to plot one of the possible
representations of a phylogeny. The vector y is a permutation of the set of leaves {1,2,. . . ,f}
compatible with the phylogeny’s topology.
Value
The function enum.phylog returns a matrix with as many columns as leaves. Each row gives a
permutation of the set of leaves {1,2,. . . ,f} compatible with the phylogeny’s topology.
Author(s)
Daniel Chessel
Sébastien Ollier 〈ollier@biomserv.univ-lyon1.fr〉
See Also
phylog