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 plotted 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 showed? 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 different cut-offs 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 2.20.1 Index]