R语言学习——韦恩图

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最新推荐文章于 2024-05-24 12:05:47 发布

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分类专栏： R语言学习文章标签： r语言学习开发语言

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limma=read.table('/Users/zhangzhishuai/Downloads/31 R韦恩图/31_venn/voom-DEG-res.txt',sep = '\t', header = T, row.names = 1)
deseq=read.table('/Users/zhangzhishuai/Downloads/31 R韦恩图/31_venn/DESeq2-DEG-res.txt',sep = '\t', header = T, row.names = 1)
edger=read.table('/Users/zhangzhishuai/Downloads/31 R韦恩图/31_venn/edger-DEG-res.txt',sep = '\t', header = T, row.names = 1)

deseq_gene=rownames(deseq)
length(deseq_gene)
limma_gene=rownames(limma)
edger_gene=rownames(edger)

# 无颜色韦恩图
library(VennDiagram)

venn.diagram(
  x = list(deseq_gene,limma_gene,edger_gene),
  category.names = c('deseq_gene', 'limma_gene', 'edger_gene'),
  filename = '/Users/zhangzhishuai/Downloads/31 R韦恩图/31_venn/gene_venn.tiff'
)

# 设置颜色
library(RColorBrewer)
mycol = brewer.pal(3,'Set1')
venn.diagram(
  x = list(deseq_gene,limma_gene,edger_gene),
  category.names = c('deseq_gene', 'limma_gene', 'edger_gene'),
  filename = '/Users/zhangzhishuai/Downloads/31 R韦恩图/31_venn/gene_venn.tiff',
  output=TRUE,
  
  # 控制输出文件大小
  height = 700,
  width = 700,
  resolution = 300, #分辨率
  compression = 'lzw', # 压缩方法
  
  #控制圆圈格式
  lwd = 1, # 控制圆圈边界的粗细
  lty = 'blank', # 控制线类型 blank:取消边界
  fill = mycol, #填充颜色
  col = mycol, #控制边界颜色
  
  #控制数字格式
  cex = 0.6, #字体大小
  
  #控制标签格式
  cat.cex = 0.4, #控制字体大小
)
 #改变填充色透明度
library(scales)
venn.diagram(
  x = list(deseq_gene,limma_gene,edger_gene),
  category.names = c('deseq_gene', 'limma_gene', 'edger_gene'),
  filename = '/Users/zhangzhishuai/Downloads/31 R韦恩图/31_venn/gene_venn.tiff',
  output=TRUE,
  
  # 控制输出文件大小
  height = 700,
  width = 700,
  resolution = 300, #分辨率
  compression = 'lzw', # 压缩方法
  
  #控制圆圈格式
  lwd = 1, # 控制圆圈边界的粗细
  lty = 'blank', # 控制线类型 blank:取消边界
  fill = c(alpha('red',0.7),alpha('blue',0.7),alpha('green',0.7)), #填充颜色 0.7指透明度
  col = mycol, #控制边界颜色
  
  #控制数字格式
  cex = 0.6, #字体大小
  
  #控制标签格式
  cat.cex = 0.4, #控制字体大小
  
)

# 各个集合的交集
inter_deseq_limma=intersect(deseq_gene,limma_gene)
length(inter_deseq_limma)

# 集合中的减法
a <- setdiff(deseq_gene,inter_deseq_limma)
length(a)
write.table(file = '/Users/zhangzhishuai/Downloads/31 R韦恩图/31_venn/test.txt',a,quote = F,
            row.names = F,# 不要行名
            col.names = F # 不要列名
            )

voom-DEG-res.txt

> head(limma)
                    logFC   AveExpr        t      P.Value    adj.P.Val          B filter
ENSG00000124208 0.6202943  8.689109 4.740494 3.960869e-04 4.130219e-03 -0.7407924      1
ENSG00000101444 0.6364420  5.259826 3.384472 4.946293e-03 2.730682e-02 -2.5863960      1
ENSG00000101333 0.5917140 10.954749 9.125611 5.542845e-07 2.534317e-05  5.5825354      1
ENSG00000078699 0.6847138  8.920357 7.674096 3.728581e-06 1.108703e-04  4.0882752      1

DESeq2-DEG-res.txt:

> head(deseq)
                 baseMean log2FoldChange      lfcSE     stat       pvalue         padj filter
ENSG00000078699 623.80574      0.5364229 0.09915439 5.409976 6.303319e-08 1.054063e-06      1
ENSG00000203880 193.28560      0.7554123 0.16557257 4.562424 5.056639e-06 6.024733e-05      1
ENSG00000124181  91.65978      1.1255133 0.21049624 5.346952 8.944770e-08 1.453515e-06      1
ENSG00000132821  23.24575      1.0751352 0.40091565 2.681699 7.324928e-03 3.482852e-02      1
ENSG00000175063  38.47452      1.9083439 0.38829445 4.914682 8.892656e-07 1.222439e-05      1

edger-DEG-res.txt

> head(edger)
                    logFC   logCPM        LR       PValue          FDR filter
ENSG00000124205 4.3068727 1.352256  6.955891 8.354367e-03 3.351821e-02      1
ENSG00000101444 0.6076843 5.332983  9.153910 2.481872e-03 1.234843e-02      1
ENSG00000206794 3.9413709 1.172266  7.859416 5.055673e-03 2.233133e-02      1
ENSG00000203880 0.7417924 7.283806 20.450844 6.118258e-06 6.250478e-05      1
ENSG00000168612 0.9946011 3.791905  6.848776 8.870204e-03 3.517956e-02      1