处理数据list

library(VennDiagram)

#导入数据，下调数据
1d <- read.table("...diff/1_DEseq2.DEG_down.xls", sep='\t', header=T)
2d <- read.table("...diff/2_DEseq2.DEG_down.xls", sep='\t', header=T)
3d <- read.table("...diff/3_DEseq2.DEG_down.xls", sep='\t', header=T)
4d <- read.table("...diff/4_DEseq2.DEG_down.xls", sep='\t', header=T)

类似地，导入 #上调数据 #全部数据

然后可以做成表，写出数据后分别查看1U2,1U2U3集合内容

#做成表
input_down  <-list(1d$gene_id,2d$gene_id,3d$gene_id,4d$gene_id)
Table_down<-calculate.overlap(input_down)

input_up  <-list(1d$gene_id,2d$gene_id,3d$gene_id,4d$gene_id)
Table_up<-calculate.overlap(input_up)

#写出投加共同上调or下调的表格
write.table(Table_down$“你需要的组合”, file = "mutually down-DESeq2.csv", sep = ",", col.names = NA,qmethod = "double")

绘制Venn图

#绘制Venn图
up<-venn.diagram(input_up,NULL, main.cex = 2,
            category = c("1d", "2d", "3d","4d"),fill = c("dodgerblue", "green", "orange", "darkorchid4"),
            alpha=0.3, cex=1.5, cat.fontface=2, cat.cex = 1, cat.col= c("dodgerblue", "green", "orange", "darkorchid4"),   imagetype = "tiff", ext.line.lty = "dotted", lty = "dotted",
            ext.line.lwd = 0.5,force.unique = F, lwd = 1, main.fontfamily="serif", main = "Up-regulated") #, filename = "Vennup.tif"

down<-venn.diagram(input_down,main.cex = 2,
            category = c("1d", "2d", "3d","4d"),fill = c("dodgerblue", "green", "orange", "darkorchid4"),
            alpha=0.3, cex=1.5, cat.fontface=2, cat.cex = 1, cat.col= c("dodgerblue", "green", "orange", "darkorchid4"), imagetype = "tiff", ext.line.lty = "dotted", lty = "dotted",
            ext.line.lwd = 0.5,force.unique = F, lwd = 1, main.fontfamily="serif", main = "Down-regulated", filename = "Venndown.tif")

分别得到一张上调Venn图和一张下调Venn图，用grid.draw()命令可以查看效果

使用pheatmap绘制heatmap

library(pheatmap)
x<-read.table("Union_for_cluster.xls", sep = "\t", header=T, row.names = 1)

x<-pheatmap(x, clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean"
        ,annotation_row = NA, cellwidth = 15,show_rownames = F, drop_levels = F
        ,clustering_method = "average", scale = "row")

#the agglomeration method should be one of "ward.D", "ward.D2", "single","complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).

把两张Venn图和一张heatmap图组合在一起

这件事费了我好大功夫啊……本来想看看Y叔有什么神奇的办法，因为自己是个半吊子，但是看了听说你还不会画heatmap以后也没学会，Y叔说可以用cowplot包，plot_grid这个函数可以拼一切基于grid的图。pheatmap是可以，但是VennDiagram生成对象是gList，用plot_grid()这个命令没办法处理gList，不停报错（差点掀桌），没办法，只好自己慢慢啃呲（谁让我是半瓶水呢）。

grid.newpage()
pushViewport(plotViewport(layout=grid.layout(2, 2,just = "centre")))
pushViewport(plotViewport(layout.pos.row=1, layout.pos.col=1))
grid.draw(up)
popViewport()
pushViewport(plotViewport(layout.pos.row=2, layout.pos.col=1, clip="on"))
grid.draw(down)
popViewport()
pushViewport(plotViewport(layout.pos.col=2, clip="inherit"))
grid.draw(x$gtable)
popViewport()

image.png

好了，因为用了自己的数据所以只能传一张高糊图片，总之最终效果就是左边2张Venn右边1张heatmap