BIC)

volcanoPlot

R Documentation

Volcano plot

Description

Volcano plot

Usage

volcanoPlot(
  data,
  log2FoldChange = "log2FoldChange",
  padj = "padj",
  colour = "red",
  saveplot = NULL,
  size = 1,
  padjLimit = 10,
  width = 13.5,
  height = 15,
  ...
)

Arguments

`data`	A dataframe.
`log2FoldChange`	Specify the columns containing log2 fold change. Default "log2FoldChange" (suitable for DESeq2 result)
`padj`	Specify the columns containing adjusted p-value. Default "padj" (suitable for DESeq2 result)
`colour`	Specify colour variable. Normally the columns containing labels to indicate if the genes are up-regulated or down-regulated or no significant difference.
`saveplot`	Save plot to given file "a.pdf", "b.png".
`size`	A number of one column name to specify point size.
`padjLimit`	Max allowed negative log10 transformed padj. Default 10.
`width`	Picture width in "cm".
`height`	Picture height in "cm".
`...`	Additional parameters given to `ggsave`.

Value

A ggplot2 object.

Examples


### Generate test data
res_output <- data.frame(log2FoldChange=rnorm(3000), row.names=paste0("ImageGP",1:3000))
res_output$padj <- 20 ^ (-1*(res_output$log2FoldChange^2))
padj = 0.05
log2FC = 1
res_output$level <- ifelse(res_output$padj<=padj,
                           ifelse(res_output$log2FoldChange>=log2FC,
                                  paste("groupA","UP"),
                                  ifelse(res_output$log2FoldChange<=(-1)*(log2FC),
                                         paste("groupB","UP"), "NoDiff")) , "NoDiff")
head(res_output)

volcanoPlot(res_output, colour="level")

Tong-Chen/ImageGP documentation built on April 14, 2025, 12:54 p.m.