TCGAbiolinks (version 1.0.10)

TCGAVisualize_volcano: Creates a volcano plot for DNA methylation or expression

Description

Creates a volcano plot from the expression and methylation analysis.

Usage

TCGAVisualize_volcano(x, y, filename = "volcano.pdf", ylab = expression(paste(-Log[10], " (FDR corrected -P values)")), xlab = NULL, title = NULL, legend = NULL, label = NULL, xlim = NULL, ylim = NULL, color = c("black", "red", "green"), names = NULL, x.cut = 0, y.cut = 0.01, height = 5, width = 10)

Arguments

x

x-axis data

y

y-axis data

filename

Filename. Default: volcano.pdf, volcano.svg, volcano.png

ylab

y axis text

xlab

x axis text

title

main title. If not specified it will be "Volcano plot (group1 vs group2)

legend

Legend title

label

vector of labels to be used in the figure. Example: c("Not Significant","Hypermethylated in group1", "Hypomethylated in group1"))#'

xlim

x limits to cut image

ylim

y limits to cut image

color

vector of colors to be used in graph

names

Names to be ploted if significant. Should be the same size of x and y

x.cut

x-axis threshold. Default: 0.0

y.cut

p-values threshold. Default: 0.01

height

Figure height

width

Figure width

Value

Saves the volcano plot in the current folder

Details

Creates a volcano plot from the expression and methylation analysis. Please see the vignette for more information Observation: This function automatically is called by TCGAanalyse_DMR

Examples

x <- runif(200, 1e5, 1e6)
y <- runif(200, 1e5, 1e6)
TCGAVisualize_volcano(x,y)