View source: R/TreeQuartetHypTest.R

quartetTestPlot | R Documentation |

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.

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

`pTable` |
table of quartets and p-values, as produced by |

`test` |
model to use, for tree null hypothesis; options are |

`alpha` |
significance level for tree test with null hypothesis given by |

`beta` |
significance level for test with null hypothesis star tree;
test results plotted only if |

`cex` |
scaling factor for size of plotted symbols |

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.

`quartetTreeTestInd`

, `quartetStarTestInd`

,
`NANUQ`

, `NANUQdist`

```
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)
```

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