双层list变成长形数据框

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绘图需求最大的难关往往是数据整理，比如下面的双层list：

set.seed(123456)
gs=list(tmp1=list(g1=sample(1000,abs(floor(100*rnorm(1)))),
 g2=sample(1000,abs(floor(100*rnorm(1))))),
 tmp2=list(g1=sample(1000,abs(floor(100*rnorm(1)))),
 g2=sample(1000,abs(floor(100*rnorm(1))))),
 tmp3=list(g1=sample(1000,abs(floor(100*rnorm(1)))),
 g2=sample(1000,abs(floor(100*rnorm(1))))))
gs

这个双层list的数据结构如下：

image-20201101184628320

有3个样本，每个样本里面都是上下调基因集合，以 g1和g2区分：

require("VennDiagram")
VENN.LIST <- lapply(gs, function(x) x$g1) 
venn.plot1 <- venn.diagram(VENN.LIST , NULL, 
 fill=c("red", "blue",'green'), 
 alpha=c(0.5,0.5,0.5), cex = 2, cat.fontface=4, 
 category.names=c('tmp1','tmp2','tmp3'), 
 main="g1 Gene Lists")
# To plot the venn diagram we will use the grid.draw() function to plot the venn diagram
grid.draw(venn.plot1)

require("VennDiagram")
VENN.LIST <- lapply(gs, function(x) x$g2) 
venn.plot2 <- venn.diagram(VENN.LIST , NULL, 
 fill=c("red", "blue",'green'), 
 alpha=c(0.5,0.5,0.5), cex = 2, cat.fontface=4, 
 category.names=c('tmp1','tmp2','tmp3'), 
 main="g2 Gene Lists")
# To plot the venn diagram we will use the grid.draw() function to plot the venn diagram
grid.draw(venn.plot2)

grid.newpage() 
grid.draw(venn.plot1)
grid.newpage() 
grid.draw(venn.plot2)

如下所示：

image-20201101184126551

韦恩图固然是一种展现方式，可以看到3个样品各自的上下调基因的overlap情况，基本上呢，随机生成的数值它们的overlap不咋地！

但是呢，3个样品我们其实更想看各自的上下调基因集的生物学功能，需要把这个双层list变成长形数据框 ，超级复杂，下面的代码：

deg=gs
deg_list=lapply(names(deg), function(y){
 tmp=deg[[y]]
 data.frame(group= paste(y,unlist(lapply(names(tmp), function(x){
 rep(x,length(tmp[[x]]))
 })),sep='_') ,
 gene=unlist(tmp))
}) 
group_g=do.call(rbind,deg_list)
group_g=do.call(rbind,deg_list)
library(org.Hs.eg.db)
group_g$gene=toTable(org.Hs.egSYMBOL)[group_g$gene,2]
head(group_g)

library(clusterProfiler)

# Convert gene ID into entrez genes
head(group_g)
tmp <- bitr(group_g$gene, fromType="SYMBOL", 
 toType="ENTREZID", 
 OrgDb="org.Hs.eg.db")

de_gene_clusters=merge(tmp,group_g,by.x='SYMBOL',by.y='gene')
table(de_gene_clusters$group)
head(de_gene_clusters)

list_de_gene_clusters <- split(de_gene_clusters$ENTREZID, 
 de_gene_clusters$group)

library(ggplot2)
gcSample= list_de_gene_clusters 
xx <- compareCluster(gcSample, fun="enrichKEGG",
 organism="hsa", pvalueCutoff=0.05)
dotplot(xx)

出图如下：

image-20201101190032371

全部的代码，复制粘贴即可运行，但是要自己写错了，需要对R语言的数据结果有比较好理解，稍微有一点点难！

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