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reproducible logo generated by ggtree

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[前端(javascript) 所属分类 前端(javascript) | 发布者 店小二04 | 时间 2016 | 作者 红领巾 ] 0人收藏点击收藏

ggtree provides many helper functions for manupulating phylogenetic trees and make it easy to explore tree structure visually.

Here, as examples, I used ggtree to draw capital character G and C , which are first letter of my name :-).

To draw a tree in such shape, we need fan layout ( circular layout with open angle) and then rotating the tree to let the open space on the correct position. Here are the source codes to produce the G and C shapes of tree. I am thinking about using the G shaped tree as ggtree logo. Have fun with ggtree :-)

library(ggtree) beast_file <- system.file("examples/MCC_FluA_H3.tree", package="ggtree") beast_tree <- read.beast(beast_file) genotype_file <- system.file("examples/Genotype.txt", package="ggtree") genotype <- read.table(genotype_file, sep="\t", stringsAsFactor=F) p <- ggtree(beast_tree, layout='circular', color="#4DAF4A", size=2, branch.length='none', right=T) + annotate('text', x=0, y=40, label='ggtree', family='mono', size=16) p2 <- gheatmap(p, genotype, width=0.2, hjust='left', colnames_angle=-10, font.size=1.5) + scale_fill_manual(values=c("#E41A1C","#377EB8","#FC8D59")) + theme_tree() open_tree(p2, 80) %>% rotate_tree(80)
reproducible logo generated by ggtree
p <- ggtree(beast_tree, layout='circular', color="#4DAF4A", size=2, branch.length='none', right=T) + xlim(-30, NA) p2 <- gheatmap(p, genotype, width=0.2, hjust='left', colnames=F) + scale_fill_manual(values=c("#E41A1C","#377EB8","#FC8D59")) + theme_tree() open_tree(p2, 90) %>% rotate_tree(50)
reproducible logo generated by ggtree
Citation

G Yu, DK Smith, H Zhu, Y Guan, TTY Lam * . ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data . Methods in Ecology and Evolution . doi:10.1111/2041-210X.12628 .

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