volcanoPlot: Volcano plot

In Tong-Chen/YSX: For Yishengxin Training

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("YSX",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/YSX documentation built on Jan. 25, 2021, 2:49 a.m.