## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) suppressPackageStartupMessages({ library(tanggle, quietly=TRUE) library(phangorn, quietly=TRUE) library(ggtree, quietly=TRUE) }) ## ----install-bioc, eval=FALSE------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("tanggle") ## ----install-gh, eval=FALSE--------------------------------------------------- # if (!requireNamespace("remotes", quietly=TRUE)) # install.packages("remotes") # remotes::install_github("KlausVigo/tanggle") ## ----install-ggtree, eval=FALSE----------------------------------------------- # remotes::install_github("YuLab-SMU/ggtree") ## ----load-pkg, echo=TRUE, results='hide'-------------------------------------- library(tanggle) library(phangorn) library(ggtree) ## ----------------------------------------------------------------------------- fdir <- system.file("extdata/trees", package = "phangorn") Nnet <- phangorn::read.nexus.networx(file.path(fdir,"woodmouse.nxs")) ## ----------------------------------------------------------------------------- p <- ggsplitnet(Nnet) + geom_tiplab2() p ## ----------------------------------------------------------------------------- p <- p + xlim(-0.019, .003) + ylim(-.01,.012) p ## ----------------------------------------------------------------------------- Nnet$translate$label <- seq_along(Nnet$tip.label) ## ----------------------------------------------------------------------------- ggsplitnet(Nnet) + geom_tiplab2(col = "blue", font = 4, hjust = -0.15) + geom_nodepoint(col = "green", size = 0.25) ## ----------------------------------------------------------------------------- ggsplitnet(Nnet) + geom_point(aes(shape=isTip, color=isTip), size=2) ## ----------------------------------------------------------------------------- z <- 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;") ## ----------------------------------------------------------------------------- ggevonet(z, layout = "rectangular") + geom_tiplab() + geom_nodelab() p <- ggevonet(z, layout = "slanted") + geom_tiplab() + geom_nodelab() p + geom_tiplab(size=3, color="purple") p + geom_nodepoint(color="#b5e521", alpha=1/4, size=10) ## ----------------------------------------------------------------------------- sessionInfo()