plot.DRdata: Plot of the dose response curves.

In HaemAalborg/DoseR: Analysis of dose response experiments

Description

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

Usage

## 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

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)

HaemAalborg/DoseR documentation built on Jan. 17, 2021, 7:40 a.m.