plotbgModel: Plot of the normalised absorbance values.

In oncoclass/DoseR: Analysis of dose response experiments

Description

Plot of the normalised absorbance values.

Usage

plotbgModel(A.data, names = NULL, drugs = NULL, times = NULL, 
            pdfit = FALSE, unit = "mol/l", logfun = "log10", 
            plots = c("Raw", "Color Corrected", 
            "Simple Correction", "Model Correction"), 
            ylab = "Absorbance", xlab = NULL, main = NULL, 
            title.1 = NULL, 
            title.2 = c("Raw", "Color Corrected", 
            "Simple Correction", "Model Correction"), 
            figure.output = file.path(getwd(), "Normalisation"), 
            col = c("#4F6E9F", "#71965A", "#9F9692", "#9D2441", 
                    "#333333", "#662D91", "#71DEC0", "#F7931E"), 
                    width = 6.69, height = NULL, pointsize = 5, 
                    cex = 1, set.par = TRUE, ...)

Arguments

A.data	The A.data object created by the function bgModel.
names	Character vector of the cell lines that are to be plotted.
drugs	Character vector of the drugs that are to be plotted.
times	Numeric vector of the times that are to be plotted.
pdfit	Logical indicating whether or not the plots should be saved in a pdf.
unit	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
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.
plots	character vector of the plots made. The value Raw plots of the raw absorbance values. The value Color Corrected plots the color corrected absorbance values. The value Simple Correction is the color and background corrected. The value Model Correction plots the model corrected absorbance values. Defeaults to c("Raw", "Color Corrected", "Simple Correction", "Model Correction").
ylab	Label for the y-axis.
xlab	Vector of labels for the x-axis
main	Vector of titles for he plot.
title.1
title.2	c("Raw", "Color Corrected", "Simple Correction", "Model Correction")
figure.output	Directory for storing the pdf files.
col	Vector of colors used for the absorbance values.
width	Numeric value indicating the width of the pdf.
height	Numeric value indicating the height of the pdf.
pointsize	Numeric value indicating the pointsize used in the pdf.
cex	Numeric value indicating the cex value used in the plot.
set.par	Logical indicater for whether or not the the number of plots per figure.
...	Further arguments passed on to the plot.

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

plotbgModelresid

Examples

require(DoseR)
data(A.data)

# Diagnostics plot of for cell line "RPMI-8226" for the drug 
# RPMI-8226" at time point 48. From left to right the plots are 
# for Raw data, colour corrected, simple background correction, 
# and model-based correction.

plotbgModel(A.data  = A.data, 
            pdfit   = FALSE,
            names   = "RPMI-8226",
            drugs   = "Doxorubicin",
            times   = 48,
            set.par = TRUE)

# The following code chunk saves the diagnostics plot for all cell lines,
# all drugs, and all times in the folder normalisation.

# plotbgModel(A.data=A.data, 
#             figure.output="Normalisation", 
#             pdfit = TRUE, 
#             pointsize = 8, 
#             set.par=TRUE)

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