绘制酷酷的火山图代码

library(canvasXpress)
# 准备数据格式 行为基因名，列为表达值，logFC, -log-pVal
  y=read.table("http://www.canvasxpress.org/data/cX-scatterR2-dat.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
  head(y)

##       AveExpr  logFC -log-pVal
## Gene1   0.940  1.399    3.5508
## Gene2   0.923  1.917    3.3186
## Gene3  -0.234 -1.150    2.8226
## Gene4   0.326 -1.329    2.7428
## Gene5   0.159 -1.050    2.5841
## Gene6   0.062 -0.896    2.4041

# 数据注释
  z=read.table("http://www.canvasxpress.org/data/cX-scatterR2-var.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
  head(z)

##       FC     Group
## Gene1  3 Increased
## Gene2  3 Increased
## Gene3  2 Decreased
## Gene4  2 Decreased
## Gene5  2 Decreased
## Gene6  2 Decreased

# 绘图
  canvasXpress(
    data=y,#数据
    varAnnot=z,#变量注释
    axisAlgorithm="rPretty",
    backgroundType="window",
    backgroundWindow="rgb(238,238,238)",
    colorBy="Group",
    colors=list("rgba(0,104,139,0.5)", "rgba(205,0,0,0.5)", "rgba(64,64,64,0.5)"),
    decorations=list(line=list(list(color="rgba(205,0,0,0.5)", width=2, x=0.5), list(color="rgba(0,104,139,0.5)", width=2, x=-0.5))),
    graphType="Scatter2D",#绘图类型
    legendBackgroundColor="rgb(238,238,238)",
    legendBox=TRUE,
    legendBoxColor="rgb(0,0,0)",
    plotBox=FALSE,
    showDecorations=TRUE,
    showTransition=TRUE,
    sizeBy="FC",
    sizes=list(4, 14, 16, 18),
    title="Volcano plot",#图片标题
    xAxis=list("logFC"),
    xAxisTickColor="rgb(255,255,255)",
    yAxis=list("-log-pVal"),
    yAxisTickColor="rgb(255,255,255)"
  )