Package 'tanggle'

geom_splitnet

Description

add splitnet layer

Usage

geom_splitnet(layout = "slanted", ...)

Arguments

layout	one of 'rectangular', 'slanted', 'circular', 'radial' or 'unrooted'
...	additional parameter

Value

splitnet layer

Author(s)

Klaus Schliep

Examples

data(yeast, package='phangorn')
dm <- phangorn::dist.ml(yeast)
nnet <- phangorn::neighborNet(dm)
ggplot(nnet, aes(x, y))  + geom_splitnet() + theme_tree()

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ggevonet

Description

drawing phylogenetic tree from phylo object

Usage

ggevonet(tr, mapping = NULL, layout = "slanted", mrsd = NULL,
  as.Date = FALSE, yscale = "none", yscale_mapping = NULL,
  ladderize = FALSE, right = FALSE, branch.length = "branch.length",
  ndigits = NULL, min_crossing = TRUE, ...)

Arguments

tr	a evonet object
mapping	aes mapping
layout	one of 'rectangular', 'slanted'
mrsd	most recent sampling date
as.Date	logical whether using Date class in time tree
yscale	y scale
yscale_mapping	yscale mapping for category variable
ladderize	logical
right	logical
branch.length	variable for scaling branch, if 'none' draw cladogram
ndigits	number of digits to round numerical annotation variable
min_crossing	logical, rotate clades to minimize crossings
...	additional parameter

Value

tree

Author(s)

Klaus Schliep

See Also

evonet, ggtree

Examples

(enet <- ape::read.evonet(text='((a:2,(b:1)#H1:1):1,(#H1,c:1):2);'))
ggevonet(enet) + geom_tiplab()
ggevonet(enet, layout = "rectangular") + geom_tiplab()

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ggsplitnet

Description

drawing phylogenetic tree from phylo object

Usage

ggsplitnet(tr, mapping = NULL, layout = "slanted", mrsd = NULL,
  as.Date = FALSE, yscale = "none", yscale_mapping = NULL,
  ladderize = FALSE, right = FALSE, branch.length = "branch.length",
  ndigits = NULL, angle = 0, ...)

Arguments

tr	a networx object
mapping	aes mapping
layout	so far only 'slanted' is supported.
mrsd	most recent sampling date
as.Date	logical whether using Date class in time tree
yscale	y scale
yscale_mapping	yscale mapping for category variable
ladderize	logical
right	logical
branch.length	variable for scaling branch, if 'none' draw cladogram
ndigits	number of digits to round numerical annotation variable
angle	rotate the plot.
...	additional parameter

Value

tree

Author(s)

Klaus Schliep

References

Schliep, K., Potts, A. J., Morrison, D. A. and Grimm, G. W. (2017), Intertwining phylogenetic trees and networks. Methods Ecol Evol. 8, 1212–1220. doi:10.1111/2041-210X.12760

Dress, A.W.M. and Huson, D.H. (2004) Constructing Splits Graphs IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 1(3), 109–115

Bagci, C., Bryant, D., Cetinkaya, B. and Huson, D.H. (2021), Microbial Phylogenetic Context Using Phylogenetic Outlines. Genome Biology and Evolution. 13(9), evab213

Potts, A.J. and Hedderson, T.A. and Grimm, G.W. (2013), Constructing Phylogenies in the Presence Of Intra-Individual Site Polymorphisms (2ISPs) with a Focus on the Nuclear Ribosomal Cistron, Systematic Biology. 63(1), 1–16

See Also

ggtree, networx, consensusNet, neighborNet

Examples

data(yeast, package='phangorn')
dm <- phangorn::dist.ml(yeast)
nnet <- phangorn::neighborNet(dm)
ggsplitnet(nnet) + geom_tiplab2()

library(phangorn)
fdir <- system.file("extdata/examples", package = "tanggle")
nymania <- read.phyDat(file.path(fdir,
           "Nymania.capensis.ITS.alignment.fasta"), format="fasta")
nnet <- neighborNet(dist.p(nymania))
ggsplitnet(nnet) + geom_tiplab2()

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minimize_overlap reduces reticulation lines crossing over in plots

Description

minimize_overlap reduces reticulation lines crossing over in plots

Usage

minimize_overlap(x)

Arguments

x	Tree of class 'evonet'

Value

A Tree with rotated nodes of class 'evonet'

Author(s)

L. Francisco Henao Diaz

Examples

fishnet <- ape::read.evonet(text='(Xalvarezi,Xmayae,((Xsignum,((Xmonticolus,
(Xclemenciae_F2,#H25)),(((((((((Xgordoni,Xmeyeri),Xcouchianus),Xvariatus),
Xevelynae),(Xxiphidium,#H24)),Xmilleri),Xandersi),Xmaculatus),(((Xmontezumae,
(Xcortezi,(Xbirchmanni_GARC,Xmalinche_CHIC2))),((Xnigrensis,Xmultilineatus),
(Xpygmaeus,Xcontinens))))#H24))),(Xhellerii)#H25));')
fishnet$edge.length <- NULL
new_tre <- minimize_overlap(fishnet)

par(mfrow=c(1,2))
ggevonet(fishnet, min_crossing = FALSE)
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, min_crossing = FALSE)
ggevonet(new_net2)

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Depth of Nodes

Description

These functions return the depths or heights of nodes and tips.

Usage

node_depth_evonet(x, ...)

Arguments

x	an object of class 'evonet'
...	Further arguments passed to or from other methods.

Value

a vector with the depth of the nodes

See Also

node.depth

Examples

z <- ape::read.evonet(text = '((1,((2,(3,(4)Y#H1)g)e,
(((Y#H1, 5)h,6)f)X#H2)c)a,((X#H2,7)d,8)b)r;')
nd <- node_depth_evonet(z)
z$edge.length <- nd[z$edge[,1]] - nd[z$edge[,2]]
ggevonet(z)

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swap_hybrid_minor

Description

Swapping the minor edges of an evonet object

Usage

swap_hybrid_minor(x, hybrid_nodes, node_times = NULL)

Arguments

x	evonet object
hybrid_nodes	a vector of hybrid nodes to have their minor edges swapped
node_times	an optional argument with node times

Value

network

Examples

(enet <- ape::read.evonet(text='((a:2,(b:1)#H1:1):1,(#H1,c:1):2);'))
ggevonet(enet) + geom_tiplab()
swapped_enet<-swap_hybrid_minor(enet,6)
ggevonet(swapped_enet) + geom_tiplab()

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