plot.PharmacoSig: Plots a PharmacoSig object into a Volcano Plot

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

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)

bhklab/PharmacoGx documentation built on April 18, 2024, 3:13 a.m.