ToxicoGx (version 0.1.1)

drugGeneResponseCurve: Compares gene expression for a specificed set of features over specific drug dosages vs time

Description

This function generates a plot visualizing the relationship between gene expression, time and dose level for the selected tSet. The plot is generated with ggplot2 and can be customized using ggplot plot + function() syntax.

Usage

drugGeneResponseCurve(
  tSet,
  duration = NULL,
  cell_lines = NULL,
  mDataTypes = NULL,
  features = NULL,
  dose = NULL,
  drug = NULL,
  summarize_replicates = TRUE,
  line_width = 1,
  point_size = 2.5,
  ggplot_args = NULL,
  verbose = TRUE
)

Arguments

tSet

ToxicoSet A ToxicoSet to be plotted in this graph. Currently only a single tSet is supported.

duration

character A vector of durations to include in the plot.

cell_lines

character A vector of cell lines to include in the plot.

mDataTypes

vector A vector specifying the molecular data types to include in this plot. Defaults to the first mDataType if not specified.ex This release version only accepts one mDataType, more to be added in forthcoming releases.

features

character A vector of feature names to include in the plot. If you specify more than two dose levels, you may only pass in up to two features.

dose

character A vector of dose levels to be included in the plot. Default to include all dose levels available for a drug. If you specify more than two features you may only pass in up to two dose levels.

drug

character A drug name to include in this plot. See drugNames(tSet) for a list of options.

summarize_replicates

logical If TRUE will average viability across replicates for each unique drug-dose-duration combination.

line_width

numeric A number specifying the thickness of lines in the plot, as passed to size in geom_line(). Defaults to 1.

point_size

numeric A number specifying how large points should be in the plot, as passed to size in geom_point(). Defaults to 2.5.

ggplot_args

list A list of ggplot2 functions which can be called using the plot + function() syntax. This allows arbitrary customization of the plot including changing the title, axis labels, colours, etc. Please see the included examples for basic usage or ggplot2 documentation for advanced customization.

verbose

boolean Should warning messages about the data passed in be printed?

Value

Plot of the viabilities for each drug vs time of exposure

Examples

# NOT RUN {
if (interactive()) {
  drugGeneResponseCurve(TGGATESsmall, dose = c("Control", "Low", "Middle"),
  mDataTypes="rna", drug = drugNames(TGGATESsmall)[1],
  duration = c("2", "8", "24"), features = "ENSG00000000003_at")
}

# }