DRdataBoxplot: Box plots of summary statistics

In oncoclass/DoseR: Analysis of dose response experiments

Description

Box plots of chosen summary statistics according to the specified dose reponse model.

Usage

DRdataBoxplot(A.data, splitvar = NULL, splitvar.col = NULL, col.all = NULL, 
              model = "G", type = "AUC", names = NULL, drug = 1, time = NULL, 
              main = NULL, ylab = NULL, clean.names = NULL, plot.order = NULL, 
              dose.scale = "mol/l", dose.logfun = "log10", ...)

Arguments

A.data	An A.data object created by the function doseResponseModel.
splitvar	Character specifying a variable according to which the boxplots should be separated e.g. a column specifying the disease origin of the cell lines.
splitvar.col	Specify the colour used for each element of splitvar.
col.all	Vector of colours. The colours are used from left to right.
model	Character specifying which dose response model the boxplot should be produced for. Currently the follwing models are implemented G, Gres, R, D, DG, and RG. Only models estimated by the function doseResponseModel can be used.
type	Character indicating the summary statistic used in the plot. This can be either of GI50, TGI, LC50, or AUC.
names	Character vector specifying the names of the cell lines that are to be plotted.
drug	Character specifying the drug to be plotted.
time	character or numeric indicator for which time point the plot is based upon. Not applicable for the model = "G"-model.
main	The main title for the plot
ylab	The label for the y-axis
clean.names	character specifying a repetitive part of cell line names that should be remove. e.g. " - inHS" if the cell lines are named as "cell.line.name - inHS".
plot.order	character vector of cell line names specifying the order of the boxplots.
dose.scale	Character indicating the scale used for concentrations when estimating the isotonic regression and the summary statistcs. The unit is written as e.g. ug/ml to indicate micro grams per milli litre and defaults to mol/l. The unit is written as ug/ml The current implementations for multiples are: Name deca hecto kilo mega giga tera peta exa zetta yotta Prefix da h k M G T P E Z Y Factor 10^0 10^1 10^2 10^3 10^6 10^9 10^12 10^15 10^18 10^21 10^24 The current implementations for fractions are: Name deci centi milli micro nano pico femto atto zepto yocto Prefix d c m u n p f a z y Factor 10^-1 10^-2 10^-3 10^-6 10^-9 10^-12 10^-15 10^-18 10^-21 10^-24
dose.logfun	Character indicating if the concentrations should be log transformed. The possible inputs are nolog for non log transformation, log10, log2, log for log transforming with base 10, 2, and e, respectively.
...	Further arguments passed along to boxplot.

Value

Box plot of bootstrapped summary statistics.

Author(s)

The function was written at department of haematology, Aalborg University Hospital and maintained by Steffen Falgreen.

References

Steffen Falgreen et al. Exposure time independent summary statistics for assessment of drug dependent cell line growth inhibition (2013)

See Also

CI,DRdataBoxplot,plot.DRdata,plot.growthModel,plotGrid

Examples

require(DoseR)
data(A.data)

DRdataBoxplot(A.data, type = "AUC", model = "G", 
         splitvar = "disease", col.all = c("#71965A", "#4F6E9F"),
         drug = "Rituximab",
         time = 48)

DRdataBoxplot(A.data, type = "AUC", model = "G", 
         splitvar = "disease", col.all = c("#71965A", "#4F6E9F"),
         drug = "Doxorubicin",
         time = 48)

oncoclass/DoseR documentation built on May 24, 2019, 2:18 p.m.