waterfall: waterfall plot Creates waterfall plot for a given drug.

In Xeva: Analysis of patient-derived xenograft (PDX) data

Description

waterfall plot Creates waterfall plot for a given drug.

Usage

waterfall(object, res.measure, drug = NULL, group.by = NULL,
  summary.stat = c(";", "mean", "median"), tissue = NULL,
  model.id = NULL, model.type = NULL, type.color = "#cc4c02",
  legend.name = NULL, yname = NULL, title = NULL, sort = TRUE)

Arguments

object	The XevaSet object
res.measure	PDX model drug response measure
drug	Name of the drug
group.by	Group drug response data
summary.stat	How to summarize multiple values
tissue	Tissue type
model.id	Indicates which model.id to plot. Default NULL will plot all models
model.type	Type of model, such as mutated or wild type
type.color	A list with colors used for each type in the legend
legend.name	Name of the legend
yname	Name for the y-axis
title	Title of the plot
sort	Default TRUE will sort the data

Value

waterfall plot in ggplot2

Examples

data(brca)
waterfall(brca, drug="binimetinib", res.measure="best.avg.response_published")
## example with model.type where we color the models by TP53 mutation type
mut <- summarizeMolecularProfiles(brca,drug = "binimetinib", mDataType="mutation")
model.type <- Biobase::exprs(mut)["TP53", ]
waterfall(brca, drug="binimetinib", res.measure="best.avg.response_published",
          tissue="BRCA", model.id=names(model.type), model.type= model.type)

Xeva documentation built on Nov. 8, 2020, 5:56 p.m.