python的世界里没有这么好的工具！

我在github上发现有一个基本上是python的讲座，因为主要是讲pandas做数据操作的，明明是个python的课，明明python也有很好的进化树可视化软件，但主讲人偏偏就讲了ggtree，并且大概说了一下，python的世界里，没有比ggtree更好的画树软件！！！以下这段话就来自于这个github repo，你可以点击阅读原文直达，有课件。

Introduction to ggtree

I deal with trees ALOT! Often these trees are to be sent to people who just want a PDF or PNG for a publication or report etc; They do not want to be playing about with analysing the tree, they simply want to look at it.

Suprisingly tools that are purpose built to visualise trees for the purpose of generating a sttic image are a bit thin on the ground.

Python has a couple of neat tools, ete3 and BioPhylo but ete3 is a bit buggy and BioPhylo is a bit ugly out of the box. They can be quite powerful and customisable but for day to day visualisations they are a bit verbose. So I use ggtree.

ggtree is an R library that is relatively straightforward and easy to use, a good workhorse for day to day use. It does have some limitations in so far as it is a little clunky if you want to add heaps of annotations and the documentation - although pretty - is light on detail and explanation. Another good thing about ggtree is that you can use many different tree formats (I will be using a simply newick today) as well as dendrograms generated by clustering.

往期精彩

• Use ggplot2

• how to bug author

• VSCode里愉快地使用R

• 功能注释后如何做富集分

• 你弱你有理，我还惹不起

• Xming-windows下远程linux桌面

• Introduction to ggplot2 and to ggtree

• use clusterProfiler as an universal enrichment analysis tool