combineCycleResolutions {MSCquartets} | R Documentation |
Combine several cycle resolutions on a tree of blobs to create a network
Description
Given a list of resolutions of different multifurcations on a tree of blobs
(each as produced by resolveCycle
), combine these with the tree
of blobs to form a network.
Usage
combineCycleResolutions(ToB, resolutions, plot = 1, titletext = NULL)
Arguments
ToB |
an unrooted tree of blobs for the network, with multifurcating nodes
labelled by |
resolutions |
a list of resolutions (each of which may be a list)
for different nodes with elements in format described in output of |
plot |
if FALSE (0), no plots; if TRUE (>0) plot networks |
titletext |
a string of text for plot |
Details
This function is useful for forming near-optimal networks when there are several resolutions that have similar fit for some of the multifurcations.
Value
a list of Newick strings for the networks, with all edge lengths 1
See Also
TINNIK
, labelIntNodes
, resolveCycle
,
resolveLevel1
Examples
data(pTableYeastRokas)
out=TINNIK(pTableYeastRokas, alpha=.01, beta=.05)
ToB=labelIntNodes(out$ToB)
R9=resolveCycle(ToB, node=9, pTable=out$pTable, alpha=.01, beta=.05, distance="NANUQ")
R10=resolveCycle(ToB, node=10, pTable=out$pTable, alpha=.01, beta=.05, distance="NANUQ")
combineCycleResolutions(ToB, resolutions=list(R9,R10),plot=TRUE)
[Package MSCquartets version 3.0 Index]