VolcanoView {MAGeCKFlute} | R Documentation

## Volcano View

### Description

Volcano plot

### Usage

    VolcanoView(df, x = "logFC", y = "adj.P.Val", Label = NA, top = 5,
      topnames = NULL, filename = NULL, x_cutoff = log2(1.5),
      y_cutoff = 0.05, main = NULL, xlab = "Log2 Fold Change",
      ylab = "-Log10(Adjust.P)", ...)

### 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).
`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.
`filename` | Figure file name to create on disk. Default filename="NULL", which means don't save the figure on disk.
`x_cutoff` | Cutoff of x-axis.
`y_cutoff` | Cutoff of y-axis.
`main` | Title of volcano figure.
`xlab` | Label of x-axis in figure.
`ylab` | Label of y-axis in figure.
`...` | Other available parameters in ggsave.

### Value

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

### Author(s)

Wubing Zhang

### Examples

    data(rra.gene_summary)
    rra = ReadRRA(rra.gene_summary)
    VolcanoView(rra, x = "LFC", y = "FDR", Label = "Official")

[Package MAGeCKFlute version 1.2.3 Index]