volcanoStatsTable {sparrow} | R Documentation

## Extracts x and y axis values from objects to create input for volcano plot

### Description

You can, in theory, create a volcano plot from a number of different parts of a `SparrowResult()` object. Most often you want to create a volcano plot from the differential expressino results, but you could imagine building a volcan plot where each point is a geneset. In this case, you would extract the pvalues from the method you like in the `SparrowResult()` object using the `stats` parameter.

### Usage

    volcanoStatsTable(
      x,
      stats = "dge",
      xaxis = "logFC",
      yaxis = "pval",
      idx = "idx",
      xtfrm = identity,
      ytfrm = function(vals) -log10(vals)
    )

### Arguments

`x` | A `SparrowResult` object, or a `data.frame`
`stats` | One of `"dge"` or `resultNames(x)`
`xaxis, yaxis` | the column of the the provided (or extracted) `data.frame` to use for the xaxis and yaxis of the volcano
`idx` | The column of the `data.frame` to use as the identifier for the element in the row. You probably don't want to mess with this
`xtfrm` | A function that transforms the `xaxis` column to an appropriate scale for the x-axis. This is the `identity` function by default, because most often the logFC is plotted as is.
`ytfrm` | A function that transforms the `yaxis` column to an appropriate scale for the y-axis. This is the `-log10(yval)` function by default, because this is how we most often plot the y-axis.

### Details

Like the `volcanoPlot()` function, this is mostly used by the sparrow.shiny package.

### Value

a `data.frame` with `.xv`, `.xy`, `.xvt` and `.xvy` columns that represent the xvalues, yvalues, transformed xvalues, and transformed yvalues, respectively

### Examples

    mg <- exampleSparrowResult()
    v.dge <- volcanoStatsTable(mg)
    v.camera <- volcanoStatsTable(mg, 'camera')

[Package sparrow version 1.0.3 Index]