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 2.10.5 Index]