TCGAVisualize_volcano {TCGAbiolinks}R Documentation

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 = "Volcano plot", 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 If you give only one number (e.g. 0.2) the cut-offs will be -0.2 and 0.2. Or you can give diffenrent cutt-ofs as a vector (e.g. c(-0.3,0.4))

y.cut

p-values threshold.

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

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

Value

Saves the volcano plot in the current folder

Examples

x <- runif(200, -1, 1)
y <- runif(200, 0.01, 1)
TCGAVisualize_volcano(x,y)
## Not run: 
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")
TCGAVisualize_volcano(x,y,filename = NULL,y.cut = 10000000,x.cut=c(-0.3,0.8),
                      names = as.character(1:length(x)), legend = "Status",
                      names.fill = TRUE, highlight = c("1","2"),show="both")

## End(Not run)
while (!(is.null(dev.list()["RStudioGD"]))){dev.off()}

[Package TCGAbiolinks version 2.12.4 Index]