quartetBTinferencePlot {MSCquartets}

Produce simplex plot with results of B/T-quartet inference

Description

Plot a 2-d probability simplex, with points for all normalized quartet count vectors. Colors indicate B- or T-quartets from TINNIK algorithm, at specified test levels.

Usage

quartetBTinferencePlot(pTable, Bquartets, test, alpha, beta, cex = 1)

Arguments

pTable

table of quartets and p-values

Bquartets

indicator vector for B-quartets (1=B, 0=T), ordered as in pTable

test

test model used for tree null hypothesis; options are "cut", "T3"

alpha

significance level used by TINNIK for test test

beta

significance level used by TINNIK for star tree test

cex

scaling factor for size of plotted symbols

Details

The first argument of this function is a table of quartets and p-values. The plot may show results using either the T3, or 2-cut test, and a star tree test. The p-values must be computed by or before previous calls to TINNIK. The second argument is the indicator vector for B/T quartets produced by TINNIK.

See Also

TINNIK, quartetTestPlot

Examples

data(pTableYeastRokas)
out=TINNIKdist(pTableYeastRokas,test="T3",alpha=.05,beta=.05)
quartetBTinferencePlot(pTableYeastRokas,out$B,test="T3",alpha=.05,beta=.05)