plotGrid: Plot of all dose reponse curves for a single drug in a panel.

In HaemAalborg/DoseR: Analysis of dose response experiments

Description

The investigation of dose response curves individually is much easier if they are plotted in individual panels with bootstrapped confidence interval shown.

Usage

plotGrid(A.data = A.data, model = "G", type = "AUC", times = NULL, 
         dose.scale = "mol/l", dose.logfun = "log10", drug = 1, 
         name = 2, names = NULL, plot.order = NULL, conc.names = NULL, 
         ylim = NULL, xlim = NULL, nrows = NULL, ncols = NULL, ylab = NULL, 
         xlab = NULL, main = paste("Dose Response Curves for", drug), 
         absorbance.CI = FALSE, absorbance.CI.col = "#C6C6C5", 
         absorbance.CI.alpha = 80, bootstrap.conf = TRUE, 
         barcol = "#71965A", bar.height = 1.3, 
         plotgrid = TRUE, grid.col = "#C6C6C5", grid.lty = 1, grid.lwd = 1, 
         bs.col = c("#333333", "#9D2441"), bs.lty = 1, bs.lwd = 0.5, 
         bs.alpha = 50, line.col = c("#333333", "#9D2441"), 
         line.lty = rep(1, 8), line.lwd = rep(1, 8), line.alpha = "", 
         col.by.identifier = TRUE, col.points = c("#333333", "#9D2441"), 
         pch = 1, plot.data = FALSE, log = "", pdfit = FALSE,
         pdf.width = 6.6929, pdf.height = 6.6929, pointsize = 8)

Arguments

A.data	An A.data object created by the function doseResponseModel.
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 to sort the pqnels. This can be either of GI50, TGI, LC50, or AUC.
times	Numeric indicator of the time points that are to be plotted.
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.
drug	Character vector of the drugs that are to be plotted.
name	When set to 2, only the the name part of the cell line is used to separate the plots.
names	The names of the cell lines to be plotted.
plot.order	The order the panels are produced. This overwrights the argument set by type.
conc.names	Names of the concentrations used in the plot. This is the names specified in the protocols.
ylim	Limit of the y-axis.
xlim	Limit of the x-axis.
nrows	The number of rows.
ncols	The number of cols.
ylab	The name of the x-axis.
xlab	The name of the x-axis.
main	The main title of the plot.
absorbance.CI	Should 95% confidence intervals for the absorbance values be shown.
absorbance.CI.col	must be specified as Hex rgb, i.e. something like "#334455".
absorbance.CI.alpha	Numeric value between 10 and 99 specifying the opacity of the confidence interval.
bootstrap.conf	Should the bootstrapped curves be shown.
barcol	Colour of the bar above each plot.
bar.height	The height of the abovementioned bar.
plotgrid	Should a grid be plotted.
grid.col	The colour of the grid.
grid.lty	Line type of the grid.
grid.lwd	Line width og the grid.
bs.col	colour of bootstrapped curves must be specified as Hex rgb, i.e. something like "#334455".
bs.lty	Line type for the bootstrapped curves.
bs.lwd	Line width of the bootstrapped curves
bs.alpha	Numeric value between 10 and 99 specifying the opacity of the bootstrap curves.
line.col	Colour of the the curves must be specified as Hex rgb, i.e. something like "#334455".
line.lty	Line type for the curves.
line.lwd	Line width for the curves.
line.alpha	Numeric value between 10 and 99 specifying the opacity of the curves.
col.by.identifier	Should the data be colourd in accordace with the specifier.
col.points	Colour of the points.
pch	The point type for the data.
plot.data	Should the data be plotted.
log	Argument passed along to the plot. if log = "y" the y-axis is log-tranformed.
pdfit	Should the created plots be save in pdfs.
pdf.width	Width of the pdf.
pdf.height	Height of te pdf.
pointsize	Pointsize of the pdf.

Value

plot of absorbance values plotted aginst time with the result of the G-model superimposed.

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

Examples

require(DoseR)
data(A.data)

# plot a grid of the dose response curves with the bootstrapped results shown 
plotGrid(A.data=A.data, barcol="#33333350",   
         ncol = 2, drug = "Doxorubicin")

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