Volcano_plot: Volcano plot for all the cytosines.

In xiaowangCN/GeneDMRs: GeneDMRs: an R package for Gene-based differentially methylated regions analysis

Volcano plot for all the cytosines.

Description

This function outputs the volcano plot for all the cytosines with Q values and methylation differences.

Usage

Volcano_plot(
  siteall_Qvalue,
  title = "Volcano for Q value and methylation difference",
  qvalue = 0.01,
  methdiffpercentage = c(5, 10, 15, 20, 25),
  pointcolor = c("red", "purple", "orange", "yellow", "blue", "green")
)

Arguments

siteall_Qvalue	refers to the input file with Q values and methylation differences.
title	refers to the figure title, with default "Volcano for Q value and methylation difference".
qvalue	refers to the threshold of Q values that Q values less than this will be colored, with default 0.01.
methdiffpercentage	refers to the threshold of methylation level ( methylation differences larger than this will be colored, with default 5, 10, 15, 20, 25.
pointcolor	refers to the point plot color, with default "red", "purple", "orange", "yellow", "blue", "green".

Value

Outputs a volcano figure.

Examples

Volcano_plot(siteall_Qvalue)
Volcano_plot(siteall_Qvalue, pointcolor = c("red", "blue", "yellow", "purple", "orange", "green"))
Volcano_plot(siteall_Qvalue, title = "Volcano plot", qvalue = 0.001, methdiffpercentage = c(10, 15, 20, 30, 40), 
pointcolor = c("red", "purple", "orange", "yellow", "blue", "green"))

xiaowangCN/GeneDMRs documentation built on Nov. 22, 2023, 11:19 p.m.