recluster (version 2.8)

recluster.plot: A plotter for recluster bootstrapped objects

Description

This function produces plots for recluster trees and assign single or pairs of support values belonging to single or multiscale analyses.

Usage

recluster.plot(tree, data, low = 1, high = 0, id=NULL, 
nodelab.cex=0.8, direction="downwards",...)

Arguments

tree

A phylo tree presumably constructed with recluster.cons function.

data

A matrix belonging to recluster.multi.

id

A vector used to mark node supports (low and high) with different colours. Such classificarion is presumably made by recluster.identify.nodes.

low

The lower scale level which bootstrap values should be indicated in the tree.

high

The higher scale level which bootstrap values should be indicated in the tree.

nodelab.cex

the cex() parameter for controlling the size of the labels on the nodes (see ?nodelabels).

direction

the direction parameter for controlling the orientation of the plot, see the ape package manual and ?plot.phylo. This parameters also controls the display of the labels on nodes.

...

Arguments to be passed to plot.phylo methods, see the ape package manual and ?plot.phylo.

Value

• A plot representing the tree with pairs of bootstrap values, below (usually x1 BP above) and high, above.

Details

This function allow to select up to two labels for nodes based on bootstrap values and optimize their layout. This is done with the nodelabels ape function, by specifying the adj parameters in the appropriate way.

References

Dapporto L., Ramazzotti M., Fattorini S., Talavera G., Vila R., Dennis R. "recluster: an unbiased clustering procedure for beta-diversity turnover" Ecography (2013), 36:1070-1075. www.unifi.it/scibio/bioinfo/recluster.html

Examples

data(datamod)
tree<-recluster.cons(datamod, tr=10)
boot<-recluster.boot(tree$cons,datamod, tr=10, boot=50)
recluster.plot(tree$cons,boot,direction="downwards")