使用UpsetR对orthofinder结果可视化

使用conda安装，使用过程中报错
查阅得知是diamond的版本不兼容导致
将diamond降级后问题解决
conda install -c bioconda diamond=0.9.14.115 (降级到0.9)

首先找到Results_XX/Orthogroups/Orthogroups.GeneCount.tsv这个文件，它记录着每个orthogroup在各个物种的基因数，由于UpsetR只接受有或无（0或1），要把全部大于0的数字替换成1

原文件

less Orthogroups.GeneCount.tsv | cut -f 1-7 | sed -r 's/\t[1-9][0-9]*/\t1/g' > gene_number.tsv

处理后

然后安装R包UpsetR

install.packages("UpSetR")
gene_number <- read.delim("D:/research/orthofinder/seq/ortho/OrthoFinder/Results_Dec02/Orthogroups/gene_number.tsv")
UpSetR::upset(gene_number,nintersects = 70,keep.order = T ,decreasing = c(T,T), sets = c("MLA","EGL","MTR","MBA","MSC","MAC"))

最后结果