TCGAbiolinks (version 1.2.5)

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, names.fill = TRUE, show.names = "significant", x.cut = 0, y.cut = 0.01, height = 5, width = 10, highlight = NULL, highlight.color = "orange", names.size = 4, dpi = 300)

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

names.fill

Names should be filled in a color box? Default: TRUE

show.names

What names will be showd? Possibilities: "both", "significant", "highlighted"

x.cut

x-axis threshold. Default: 0.0

y.cut

p-values threshold. Default: 0.01

height

Figure height

width

Figure width

highlight

List of genes/probes to be highlighted. It should be in the names argument.

highlight.color

Color of the points highlighted

names.size

Size of the names text

dpi

Figure dpi

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, -1, 1)
y <- runif(200, 0.01, 1)
TCGAVisualize_volcano(x,y)
TCGAVisualize_volcano(x,y,filename = NULL,y.cut = 10000000,x.cut=0.8,
                      names = rep("AAAA",length(x)), legend = "Status",
                      names.fill = FALSE)
TCGAVisualize_volcano(x,y,filename = NULL,y.cut = 10000000,x.cut=0.8,
                      names = as.character(1:length(x)), legend = "Status",
                      names.fill = TRUE, highlight = c("1","2"),show="both")
while (!(is.null(dev.list()["RStudioGD"]))){dev.off()}