drugGeneResponseCurve {ToxicoGx} | R Documentation |
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
if (interactive()) {
drugGeneResponseCurve(TGGATESsmall, dose = c("Control", "Low", "Middle"),
mDataTypes="rna", drug = drugNames(TGGATESsmall)[1],
duration = c("2", "8", "24"), features = "ENSG00000002726_at")
}
[Package
ToxicoGx version 1.3.5
Index]