plot.DRdata: Plot of the dose response curves.

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

View source: R/plotfunctions.R

Description

Plot of the dose response curves according to the specified model.

Usage

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## S3 method for class 'DRdata'
plot(x, ..., drug = 1, 
     ylim = NULL, xlim = NULL, main = drug, 
     plot.data = FALSE, model = "G", type = "AUC", 
     ylab = NULL, xlab = NULL, cex = 1, names = NULL, 
     times = NULL, col.scheme = NULL,
     color.palette = "Dark2", n.colors = NULL, 
     reverse.col = FALSE, col = NULL, lty = NULL, pch = NULL, 
     lwd = 2, legend.place = "bottomleft", plot.order = NULL, 
     dose.scale = "mol/l", dose.logfun = "log10", legend = TRUE, 
     n.columns = 2, legend.cex = 1, use.col.order = FALSE, split = "all")

Arguments

x

An A.data object created by the function doseResponseModel.

...

Further arguments passed to plot.

drug

Character specifying the drug to be plotted.

ylim

Limits of the y-axis

xlim

Limits of the x-axis

main

Main title of the plot.

plot.data

Should the data be plotted along with the fitted curves.

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.

ylab

Name of the y-axis

xlab

Name of the x-axis

cex

Specify cex for the plot.

names

Character vector of the cell line names used in the plot.

times

Numeric vector specifying the timepoints the dose response curves should be based upon.

col.scheme

Specific colscheme used. A number of colours to choose from when generating the plot.

color.palette

The colour palette used for generating colours defeaults to "Dark2"

n.colors

Numeric indicator for the number of colours to use.

reverse.col

should the automatically generated colours be reversed.

col

Vector of colours.

lty

Numeric value for line of type.

pch

Numeric value for type of points.

lwd

Numeric value for line width

legend.place

Where should the legend be placed: "bottomleft" is defeault.

plot.order

Character vector of names specifying the order the cell lines should be plotted. Can be used in combination with the argument use.col.order to colour each cell line specifically.

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.

legend

Should a legend be created.

n.columns

The number of columns in the legend.

legend.cex

numeric indicator for the size of the legend.

use.col.order

Should the colours specified be used in the order by which they are given.

split

Character specifying a variable according to which the dose response curves should be separated e.g. a column specifying the disease origin of the cell lines.

Value

Dose response curves according to the specifyed model.

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)

par(mfrow = c(1,2))
plot.DRdata(x          = A.data,
            model      = "D",
            col.scheme =  c("#71965A", "#4F6E9F"),
            drug       = "Doxorubicin",
            legend     = TRUE,
            n.columns  = 1, 
            plot.data  = TRUE,
            legend.cex = 1, 
            times      = c(12, 24, 36, 48))

plot.DRdata(x          = A.data,
            model      = "D",
            col.scheme =  c("#71965A", "#4F6E9F"),
            drug       = "Rituximab",
            legend     = TRUE,
            n.columns  = 1, 
            plot.data  = TRUE,
            legend.cex = 1, 
            times      = c(12, 24, 36, 48))

par(mfrow = c(1,2))

plot.DRdata(x     = A.data,
            model = "G", 
            drug  = "Rituximab",
            col.scheme =  c("#71965A", "#4F6E9F"),
            n.columns  = 1,
            plot.data  = TRUE,legend = TRUE,
            legend.cex = 1)

plot.DRdata(x     = A.data,
            model = "G", 
            drug  = "Doxorubicin",
            col.scheme =  c("#71965A", "#4F6E9F"),
            n.columns  = 1,
            plot.data  = TRUE,legend = TRUE,
            legend.cex = 1)

oncoclass/DoseR documentation built on Nov. 23, 2017, 4:12 a.m.