VolcanoView {MAGeCKFlute} | R Documentation

## Volcano View

### Description

Volcano plot

### Usage

    VolcanoView(
      df,
      x = "logFC",
      y = "adj.P.Val",
      Label = NA,
      top = 5,
      topnames = NULL,
      x_cutoff = log2(1.5),
      y_cutoff = 0.05,
      mycolour = c("gray80", "#e41a1c", "#377eb8"),
      alpha = 0.6,
      force = 0.1,
      main = NULL,
      xlab = "Log2 Fold Change",
      ylab = "-Log10(Adjust.P)",
      filename = NULL,
      width = 4,
      height = 2.5,
      ...
    )

### Arguments

`df` | Data frame
`x` | Colname of df specifying x-axis in Volcanno figure, 'logFC' (default).
`y` | Colname of df specifying y-axis in Volcanno figure, 'adj.P.Val' (default), which will be plot after log10 transformation.
`Label` | Colname of df specifying labeled terms in Volcanno figure.
`top` | Interger, the number of top significant terms to be labeled.
`topnames` | Character vector, indicating interested terms to be labeled.
`x_cutoff` | Cutoff of x-axis.
`y_cutoff` | Cutoff of y-axis.
`mycolour` | A color vector, specifying colors of non-significant, significant up and down-regulated genes.
`alpha` | Parameter in ggplot.
`force` | Parameter for geom_text_repel.
`main` | Title of volcano figure.
`xlab` | Label of x-axis in figure.
`ylab` | Label of y-axis in figure.
`filename` | Figure file name to create on disk. Default filename="NULL", which means don't save the figure on disk.
`width` | Width of figure.
`height` | Height of figure.
`...` | Other available parameters in ggsave.

### Value

An object created by `ggplot`, which can be assigned and further customized.

### Author(s)

Wubing Zhang

### Examples

    file1 = file.path(system.file("extdata", package = "MAGeCKFlute"),
    "testdata/rra.gene_summary.txt")
    gdata = ReadRRA(file1)
    VolcanoView(gdata, x = "Score", y = "FDR", Label = "id")

[Package MAGeCKFlute version 1.12.0 Index]