plot.PharmacoSig {PharmacoGx} | R Documentation

## Plots a PharmacoSig object into a Volcano Plot

### Description

Given a PharmacoSig, this will plot a volcano plot, with parameters to set cutoffs for a significant effect size, p value, to pick multiple testing correction strategy, and to change point colors. Built on top of ggplot, it will return the plot object which can be easily customized as any other ggplot.

### Usage

    ## S3 method for class 'PharmacoSig'
    plot(
      x,
      adjust.method,
      drugs,
      features,
      effect_cutoff,
      signif_cutoff,
      color,
      ...
    )

### Arguments

`x` | `PharmacoSig` a PharmacoSig object, result of drugSensitivitySig or drugPerturbationSig
`adjust.method` | `character(1)` or `logical(1)` either FALSE for no adjustment, or one of the methods implemented by p.adjust. Defaults to FALSE for no correction
`drugs` | `character` a vector of drug names for which to plot the estimated associations with gene expression
`features` | `character` a vector of features for which to plot the estimated associations with drug treatment
`effect_cutoff` | the cutoff to use for coloring significant effect sizes.
`signif_cutoff` | the cutoff to use for coloring significance by p value or adjusted p values. Not on log scale.
`color` | one color if no cutoffs set for plotting. A vector of colors otherwise used to color points the in three categories above.
`...` | additional arguments, not currently used, but left here for consistency with plot

### Value

returns a ggplot object, which by default will be evaluated and the plot displayed, or can be saved to a variable for further customization by adding ggplot elements to the returned graph

### Examples

    data(GDSCsmall)
    drug.sensitivity <- drugSensitivitySig(GDSCsmall, mDataType="rna",
                 nthread=1, features = fNames(GDSCsmall, "rna")[1])
    plot(drug.sensitivity)

[Package PharmacoGx version 2.4.0 Index]