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Last data update: 2014.03.03

R: Creates a volcano plot for DNA methylation or expression

TCGAVisualize_volcano

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 = 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

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)
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()}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(TCGAbiolinks)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TCGAbiolinks/TCGAVisualize_volcano.Rd_%03d_medium.png", width=480, height=480)
> ### Name: TCGAVisualize_volcano
> ### Title: Creates a volcano plot for DNA methylation or expression
> ### Aliases: TCGAVisualize_volcano
> 
> ### ** 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")
[1] 1 2
> while (!(is.null(dev.list()["RStudioGD"]))){dev.off()}
> 
> 
> 
> 
> 
> dev.off()
Error in dev.off() : cannot shut down device 1 (the null device)
Execution halted