r语言 断轴 画图_【教程】使用R语言画lineage though time plot (LTT)

#load ape package

library('ape')

#read a selected trees file; select nexus trees file in pumped

window, and name it as treesForLTT

read.nexus(choose.files())->treesForLTT

#read one tree (the best tree)

read.nexus(choose.files())->oneTreeForLTT

#check how many trees are there in treesForLTT

treesForLTT

#burn some trees.30% of total trees is acceptable. Set your

own number.

treesForLTT[3000:10001]->fineTreesForLTT

#It could be slow if there are too many trees. Discard more

trees will help.

#预画图

#draw LTT plot of all fine trees.

mltt.plot(fineTreesForLTT, legend = F, dcol = F, ylab =

'Number of Lineages', xlab = 'Time')

#add the best tree

ltt.lines(oneTreeForLTT, col = 'red', lwd = 2)

得到图片如下：

图太长了。因为一些树左边的枝太长太长。另外，黑色太厚实了，不好看。

#重写mltt.plot函数并修图

#添加了两个参数，xrange限制x轴的范围；owncol指定线的颜色。

#the x axis is so long. Has to be black in mltt.plot?

#Don't know how to change xlim and line color in mltt. So

stupid am I.

#so rewrite function mltt.plot into Own.mltt.plot</