注册 登录  
 加关注
   显示下一条  |  关闭
温馨提示!由于新浪微博认证机制调整,您的新浪微博帐号绑定已过期,请重新绑定!立即重新绑定新浪微博》  |  关闭

wangyufeng的博客

祝愿BB 健康开心快乐每一天

 
 
 

日志

 
 

How to draw Venn diagrams from differential gene expression data  

2013-09-18 16:42:44|  分类: R、SVG&GNUPlot画 |  标签: |举报 |字号 订阅

  下载LOFTER 我的照片书  |

Venn diagrams is commonly used to visualize the overlapping among data sets, including differential gene expression data under various condition. Here I shaw you one way to draw venn diagram (see below) in R using VennDiagram package using data generated from DESeq.

How to draw Venn diagrams from differential gene expression data - 喜欢吃桃子 - wangyufeng的博客

 

THRESHOLD <- 0.05
A.cds.sig <- subset(A.cds.result, pval<THRESHOLD) ## A.cds.result was generated from DESeq
B.cds.sig <- subset(B.cds.result, pval<THRESHOLD) ## B.cds.result was generated from DESeq
 
library(VennDiagram)
pdf("venn_diagram.pdf")
venn.plot <- venn.diagram(list(A.cds.sig$id, B.cds.sig$id), NULL, fill=c("red", "green"), alpha=c(0.5,0.5), cex = 2, cat.fontface=4, category.names=c("Condition A", "Condition B"))
grid.draw(venn.plot)
dev.off()

Here I used grid::grid.draw function to generate the PDF, because the venn.diagram complains generating PDF. I have manually changed the position and font size of the category legends in the figure above. However, there are some parameters you can adjust in the venn.diagram function to set the legends, layout, transparency (alpha-channel), etc.

 

more information pls link to:http://biobeat.wordpress.com/category/tips/

  评论这张
 
阅读(1024)| 评论(0)
推荐 转载

历史上的今天

在LOFTER的更多文章

评论

<#--最新日志,群博日志--> <#--推荐日志--> <#--引用记录--> <#--博主推荐--> <#--随机阅读--> <#--首页推荐--> <#--历史上的今天--> <#--被推荐日志--> <#--上一篇,下一篇--> <#-- 热度 --> <#-- 网易新闻广告 --> <#--右边模块结构--> <#--评论模块结构--> <#--引用模块结构--> <#--博主发起的投票-->
 
 
 
 
 
 
 
 
 
 
 
 
 
 

页脚

网易公司版权所有 ©1997-2017