drugDoseResponseCurve: Plot drug response curve of a given drug and a given cell for...

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

Plot drug response curve of a given drug and a given cell for a list of pSets (objects of the PharmacoSet class).

Description

Given a list of PharmacoSets, the function will plot the drug_response curve, for a given drug/cell pair. The y axis of the plot is the viability percentage and x axis is the log transformed concentrations. If more than one pSet is provided, a light gray area would show the common concentration range between pSets. User can ask for type of sensitivity measurment to be shown in the plot legend. The user can also provide a list of their own concentrations and viability values, as in the examples below, and it will be treated as experiments equivalent to values coming from a pset. The names of the concentration list determine the legend labels.

Usage

drugDoseResponseCurve(
  drug,
  cellline,
  pSets = list(),
  concentrations = list(),
  viabilities = list(),
  conc_as_log = FALSE,
  viability_as_pct = TRUE,
  trunc = TRUE,
  legends.label = c("ic50_published", "gi50_published", "auc_published",
    "auc_recomputed", "ic50_recomputed"),
  ylim = c(0, 100),
  xlim,
  mycol,
  title,
  plot.type = c("Fitted", "Actual", "Both"),
  summarize.replicates = TRUE,
  lwd = 0.5,
  cex = 0.7,
  cex.main = 0.9,
  legend.loc = "topright",
  verbose = TRUE,
  sample_col = "sampleid",
  treatment_col = "treatmentid"
)

Arguments

drug	character(1) A drug name for which the drug response curve should be plotted. If the plot is desirable for more than one pharmaco set, A unique drug id should be provided.
cellline	character(1) A cell line name for which the drug response curve should be plotted. If the plot is desirable for more than one pharmaco set, A unique cell id should be provided.
pSets	list a list of PharmacoSet objects, for which the function should plot the curves.
concentrations, viabilities	list A list of concentrations and viabilities to plot, the function assumes that concentrations[[i]] is plotted against viabilities[[i]]. The names of the concentration list are used to create the legend labels
conc_as_log	logical, if true, assumes that log10-concentration data has been given rather than concentration data, and that log10(ICn) should be returned instead of ICn. Applies only to the concentrations parameter.
viability_as_pct	logical, if false, assumes that viability is given as a decimal rather than a percentage, and that E_inf passed in as decimal. Applies only to the viabilities parameter.
trunc	logical(1) Should the viability values be truncated to lie in [0-100] before doing the fitting
legends.label	numeric A vector of sensitivity measurment types which could be any combination of ic50_published, auc_published, auc_recomputed and auc_recomputed_star. A legend will be displayed on the top right of the plot which each line of the legend is the values of requested sensitivity measerments for one of the requested pSets. If this parameter is missed no legend would be provided for the plot.
ylim	numeric A vector of two numerical values to be used as ylim of the plot. If this parameter would be missed c(0,100) would be used as the ylim of the plot.
xlim	numeric A vector of two numerical values to be used as xlim of the plot. If this parameter would be missed the minimum and maximum comncentrations between all the pSets would be used as plot xlim.
mycol	numeric A vector with the same lenght of the pSets parameter which will determine the color of the curve for the pharmaco sets. If this parameter is missed default colors from Rcolorbrewer package will be used as curves color.
title	character The title of the graph. If no title is provided, then it defaults to 'Drug':'Cell Line'.
plot.type	character Plot type which can be the actual one ("Actual") or the one fitted by logl logistic regression ("Fitted") or both of them ("Both"). If this parameter is missed by default actual curve is plotted.
summarize.replicates	character If this parameter is set to true replicates are summarized and replicates are plotted individually otherwise
lwd	numeric The line width to plot with
cex	numeric The cex parameter passed to plot
cex.main	numeric The cex.main parameter passed to plot, controls the size of the titles
legend.loc	And argument passable to xy.coords for the position to place the legend.
verbose	logical(1) Should warning messages about the data passed in be printed?
sample_col	character(1) The name of the column in the profiles assay that contains the sample IDs.
treatment_col	character(1) The name of the column in the profiles assay that contains the treatment IDs.

Value

Plots to the active graphics device and returns an invisible NULL.

Examples

if (interactive()) {
# Manually enter the plot parameters
drugDoseResponseCurve(concentrations=list("Experiment 1"=c(.008, .04, .2, 1)),
 viabilities=list(c(100,50,30,1)), plot.type="Both")

# Generate a plot from one or more PSets
data(GDSCsmall)
drugDoseResponseCurve(drug="Doxorubicin", cellline="22RV1", pSets=GDSCsmall)
}

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