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

In MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

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)

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.