DRdataBoxplot: Box plots of summary statistics

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/plotfunctions.R

Description

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

Usage

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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

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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 Nov. 23, 2017, 4:12 a.m.