quartetTestPlot: Produce simplex plot with results of quartet hypothesis tests

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

Produce simplex plot with results of quartet hypothesis tests

Description

Plot a 2-d probability simplex, with points for all quartet count vectors. Colors indicate rejection or failure to reject for tests at specified levels.

Usage

quartetTestPlot(pTable, test, alpha = 0.05, beta = 1, cex = 1)

Arguments

pTable	table of quartets and p-values, as produced by quartetTreeTestInd, quartetStarTestInd, or NANUQ
test	model to use, for tree null hypothesis; options are "T1", "T3", "cut", "NANUQ"
alpha	significance level for tree test with null hypothesis given by test
beta	significance level for test with null hypothesis star tree; test results plotted only if beta<1 and "p_star" column present in pTable
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 of either the T1, T3, or 2-cut test, with or without a star tree test (depending on whether a "p_star" column is in the table and/or beta =1). The p-values must be computed by previous calls to quartetTreeTestInd (for "T1" or "T3" p-values) and quartetStarTestInd (for "star" p-values). The NANUQ and NANUQdist functions include calls to these tree test functions.

See Also

quartetTreeTestInd, quartetStarTestInd, NANUQ, NANUQdist

Examples

gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=c("t1","t2","t3","t4","t5","t6")
QT=quartetTable(gtrees,tnames[1:6])
RQT=quartetTableResolved(QT)
stree="(((t5,t6),t4),((t1,t2),t3));"
pTable=quartetTreeTestInd(RQT,"T1",speciestree=stree)
pTable=quartetStarTestInd(pTable)
quartetTestPlot(pTable, "T1", alpha=.05, beta=.95)

MSCquartets documentation built on Nov. 2, 2023, 5:32 p.m.