EnhancedVolcano-一个可个性化火山图的R包

一般我们用ggplot2 绘火山图 ，但是ggplot2对于R初学者来说配置是很复杂的。EnhancedVolcano是一个使用极其简单的火山图绘制包。

# 安装EnhancedVolcano
  if (!requireNamespace('BiocManager', quietly = TRUE))
    install.packages('BiocManager')

  BiocManager::install('EnhancedVolcano')

# 或者
  devtools::install_github('kevinblighe/EnhancedVolcano')

下面通过一个示例来演示：

library(airway)
library(magrittr)
library("DESeq2")

# 加载演示数据
data("airway")
airway$dex %<>% relevel("untrt")

# DESeq2计算差异
dds <- DESeqDataSet(airway, design = ~ cell + dex)
dds <- DESeq(dds, betaPrior = FALSE)
res1 <- results(dds, contrast = c("dex", "trt", "untrt"))
res1 <-
  lfcShrink(dds,
            contrast = c("dex", "trt", "untrt"),
            res = res1)
res2 <- results(dds, contrast = c("cell", "N061011", "N61311"))
res2 <-
  lfcShrink(dds,
            contrast = c("cell", "N061011", "N61311"),
            res = res2)


  EnhancedVolcano(res2,
    lab = rownames(res2),
    x = 'log2FoldChange',
    y = 'pvalue',
    selectLab = c('ENSG00000106565','ENSG00000187758'),
    xlim = c(-6,7),
    xlab = bquote(~Log[2]~ 'fold change'),
    pCutoff = 10e-14,
    FCcutoff = 2.0,
    pointSize = 4.0,
    labSize = 5.0,
    boxedLabels = T,
    shape = c(4, 35, 17, 18),
    colAlpha = 1,
    legendPosition = 'right',
    legendLabSize = 9,
    legendIconSize = 5.0)

参考资料：

1.http://www.bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html