minimize_overlap: minimize_overlap reduces reticulation lines crossing over in...
In KlausVigo/ggnetworx: Visualization of Phylogenetic Networks

Description Usage Arguments Value Author(s) Examples

View source: R/minimize_overlap.R

minimize_overlap reduces reticulation lines crossing over in plots

1	minimize_overlap(x)

`x`	Tree of class 'evonet'

A Tree with rotated nodes of class 'evonet'

L. Francisco Henao Diaz

fishnet <- ape::read.evonet(text="(Xalvarezi,Xmayae,((Xsignum,((Xmonticolus,(Xclemenciae_F2,#H25:::0.032485577051040423):0.979116879342896):1.4858786525152954,(((((((((Xgordoni,Xmeyeri):0.26111415598145865,Xcouchianus):3.5325554148283564,Xvariatus):0.6445452395880061,Xevelynae):0.41219807813960146,(Xxiphidium,#H24:0.0::0.16538333427567822):1.4020042304402076):0.2921320715527958,Xmilleri):0.4688709909949548,Xandersi):0.6492623942884177,Xmaculatus):1.0200542801748702,(((Xmontezumae,(Xcortezi,(Xbirchmanni_GARC,Xmalinche_CHIC2):0.8943004029517725):0.6903622798656042):0.4926275928330048,((Xnigrensis,Xmultilineatus):1.4508210422790195,(Xpygmaeus,Xcontinens):1.9686498919562234):2.428065080719157):2.0435103751744865)#H24:0.6476450483433508::0.8346166657243218):0.7816554661308311):1.9841381634366537):0.31614675520900004,(Xhellerii)#H25:::0.9675144229489596):0.28226883225049243);")
fishnet$edge.length <- NULL
new_tre <- minimize_overlap(fishnet)

par(mfrow=c(1,2))
ggevonet(fishnet)
ggevonet(new_tre)

net2 <- ape::read.evonet(text="(15,(1,((14,(#H1,(((12,13),(11,#H3)),(7,
   ((10)#H3,(8,9)))))),((((2,3))#H2,(6,(5,(#H2,4)))))#H1)));")
# Cui et al. 2013 Evol.
new_net2 <- minimize_overlap(net2)
ggevonet(net2)
ggevonet(new_net2)