In KlausVigo/ggnetworx: Visualization of Phylogenetic Networks

knitr::opts_chunk$set(echo = TRUE, warning = FALSE)

tanggle usage examples

You can use "tanggle" with other tree visualization packages such as ggimage. Here is an example phylogenetic network with images:

Calling neccessery packages/libraries:

library(ape)
library(ggtree)
library(ggimage)
library(ggnetworx)

Reading/creating networks

whalesnet = read.evonet(text="(((balMys,Egl00):9.055782863234407)#H13:2.6340479153169807::0.8331903627712247,(Bac00,(((Bbo01,Bbo02):9.41949690722463,(Bmu,#H:0.0::0.013010091110208823)):1.6484045144986545,((#H13:0.19346605673125924::0.16680963722877526,((Erob02,Erob01):1.7595289284120899)#H:8.238071084864815::0.9869899088897912):0.35164828246609625,(Mno00,Bph03):2.146642742731017):0.066043783465627):1.100383484076166):2.6340479153169807);")

Creating species names/labels

label <- whalesnet$tip.label 
whalesnet$edge.length <- NULL

and create path to the images

fdir <- system.file("extdata/pics", package = "ggnetworx")

ggevonet(whalesnet,layout = "slanted") +
    xlim(NA, 17)  + 
    geom_tiplab(aes(image=file.path(fdir, paste0(label, '.png'))), geom="image",
                offset=2, align=1.5, size=.15) +
    geom_tiplab(geom='label', offset=.5, hjust=.1)