README.md

In helloicyvodka/ggVITA: An R package for VIsualization and annotation of Tree Alignment.

ggvita (visualization of tree alignments)

Sun Yat-sen University (SYSU), Evolution and Genomics Function Lab, Chen&Yang Lab

Authors : Jianrong Philip Yang , Meng Yuan , Xiaolong Cao

Date : 2017-10-10

ggvita,an R package, is developed for visualization of tree alignment results based on ggtree and ggplot2 packages. Pro. Jianrong Philip Yang designed an algorithm to calculate the similarity between trees. This algorithm can dectect tree similar phenotypes at the sub tree scale.These results connect genotypes with phenotypes during a binary-tree development, from single cell ( usually zygote ) to multiple cells. When we connect genotypes with phenotypes of livings, we can observe some interesting phenomena and find out the biology mechanisms behind them. stat_epic function can add expression levels of genes from EPIC (http://epic.gs.washington.edu/) on the branches of trees alignment results.

Installation

Method 1 (User Method):

install.packages("devtools")  
install_github("helloicyvodka/ggvita")  
library(ggvita)  

Method 2 (Developer Method):

Linux shell:

$ git clone "http://...."  

R console:

load_all(the_file_cloned_to)  

If there is any problem, welcome to email me.

helloicyvodka/ggVITA documentation built on May 28, 2019, 8:55 p.m.