volcanoPlot {sparrow} | R Documentation

## Create an interactive volcano plot

### Description

Convenience function to create volcano plots from results generated within this package. This is mostly used by `{sparrow.shiny}`.

### Usage

    volcanoPlot(
      x,
      stats = "dge",
      xaxis = "logFC",
      yaxis = "pval",
      idx,
      xtfrm = base::identity,
      ytfrm = function(vals) -log10(vals),
      xlab = xaxis,
      ylab = sprintf("-log10(%s)", yaxis),
      highlight = NULL,
      horiz_line = c(padj = 0.1),
      xhex = NULL,
      yhex = NULL,
      width = NULL,
      height = NULL,
      shiny_source = "mgvolcano",
      ggtheme = ggplot2::theme_bw(),
      ...
    )

### Arguments

`x` | A `SparrowResult` object, or a `data.frame`
`stats` | One of `"dge"` or `resultNames(x)`
`xaxis` | the column of the the provided (or extracted) `data.frame` to use for the xaxis and yaxis of the volcano
`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.
`xlab, ylab` | x and y axis labels
`highlight` | A vector of featureIds to highlight, or a GeneSetDb that we can extract the featureIds from for this purpose.
`horiz_line` | A (optionally named) number vecor (length 1) that indicates where a line should be drawn across the volcano plot. This is usually done to signify statistical significance. When the number is "named", this indicates that you want to find an approximation of the values plotted on y based on some transformation of the values that is the named column of x (like "padj"). The default value `c(padj = 0.10)` indicates you want to draw a line at approximately where the adjust pvalue of 0.10 is on the y-axis, which is the nominal pvalues.
`xhex` | The raw `.xv` (not `xtfrm(.xv)`) value that acts as a threshold such that values less than this will be hexbinned.
`yhex` | the `.yvt` value threshold. Vaues less than this will be hexbinned.
`width` | the width and height of the output plotly plot
`height` | the width and height of the output plotly plot
`shiny_source` | the name of this element that is used in shiny callbacks. Defaults to `"mggenes"`.
`ggtheme` | a ggplot theme, like the thing returned from `ggplot2::theme_bw()`, for instance.
`...` | pass through arguments (not used)

### Value

a ploty plot object

### Examples

    mg <- exampleSparrowResult()
    volcanoPlot(mg)
    volcanoPlot(mg, xhex=1, yhex=0.05)

[Package sparrow version 1.0.3 Index]