buildVolcanoPlot: Build a volcano plot of biomarkers

In EvgeniyaGorobets/PGxVision: Visualize Biomarkers and Pharmacogenomic Data

Description

Note that this volcano plot is NOT plotting results of differential gene expression analysis but is plotting the drug sensitivity signature (drug sensitivity estimate on x-axis and log10(p-value) on y-axis). Points are colored based on significance (red = significant; gray = not significant). Currently, only a single experiment (one tissue, one compound, one molecular data type) can be plotted at once.

Usage

buildVolcanoPlot(
  biomarkerDf,
  tissue = "",
  compound = "",
  mDataType = "",
  pValCutoff = 0.05,
  xLabel = NULL,
  yLabel = NULL,
  title = NULL
)

Arguments

biomarkerDf	A data.frame of drug sensitivity biomarkers that you want to plot, including the compound, tissue, molecular data type ("mDataType"), drug sensitivity estimate ("estimate") and p-value ("pvalue")
tissue	A string representing the tissue for which you want to plot biomarker drug sensitivity signatures
compound	A string representing the compound for which you want to plot biomarker drug sensitivity signatures
mDataType	A string representing the molecular data type for which you want to plot biomarker drug sensitivity signatures
pValCutoff	(optional) A number between 0 and 1 indicating the maximum p-value that an experimental result can have to be considered significant. Any results with a higher p-value will be grayed out on the plot. Default value is 0.05.
xLabel	(optional) The label for the x-axis. Defaults to "Estimate".
yLabel	(optional) The label for the y-axis. Defaults to "Log10 P-Value".
title	(optional) The title for the plot. Defaults to "Drug sensitivity in <tissueName> tissue in response to <compoundName>

Value

A named list with two fields: "dt" and "plot". The "plot" field contains a ggplot2 plot object (the volcano plot) and the "dt" field contains a data.table with all the biomarkers that were plotted on "plot"

Examples

data(Biomarkers)
result <- buildVolcanoPlot(Biomarkers, "Lung", "Trametinib", "rna", 0.005)
result$dt
result$plot

EvgeniyaGorobets/PGxVision documentation built on Dec. 17, 2021, 7:26 p.m.