plotbgModel: Plot of the normalised absorbance values.

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

View source: R/plotfunctions.R

Description

Plot of the normalised absorbance values.

Usage

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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

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