plotdrugColorCorrection: Plot the result of drug color correction.
In HaemAalborg/DoseR: Analysis of dose response experiments

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

Three types of plots can be generated using the function specified by the plot.type. A plot of the estimated absorbance measures is produced when plot.type = "raw". Finally, when plot.type = "output" the drug specific absorbance associated with each concentration is plotted against the concentration.

plotdrugColorCorrection(A.data, file = file.path(getwd(), "drugColorCorrection.pdf"), 
                         drugs = NULL, pdfit = FALSE, width = 7, height = 3.5, 
                         type.plot = c("output", "raw"), xlab = NULL, ylab = NULL,
                         main = NULL, xlim = NULL, ylim = NULL, 
                         col = c("#71965A", "#4F6E9F", "#9F9692", "#9D2441",
                                 "#333333", "#662D91", "#71DEC0", "#F7931E"),
                         col.plate = TRUE, set.par = FALSE, ...)

`A.data`	An A.data object created by the function `drugColorCorrection`.
`file`	Character specifying the pdf file for saving the resulting plots.
`drugs`	Character vector specifying the drugs for which the plot should be made. Defeaults to `NULL` where plots for all drugs are created.
`pdfit`	Logical indicating whether or not the plots should be saved in a pdf.
`width`	Numeric value specifying the width of the pdf in inches.
`height`	Numeric value specifying the height of the pdf in inches.
`type.plot`	Character specifying the type of plot to be made. Currently the implemented types are 1) `"output"` which produces a plot of the estimated drug specific absorbances and 2 ) `"raw"` which produces a plot of the normalised absorbace measures.
`xlab`	Character specifying the the x-axis label.
`ylab`	Character specifying the the y-axis label. For `plot.type = "output"` this should be a vector of length three.
`main`	The main title of the plots.
`xlim`	Numeric vector for the range of the x-axis.
`ylim`	Numeric vector for the range of the y-axis.
`col`	Vector of colours.
`col.plate`	With `type.plot = c("raw")` should the colour set per plate. Defeault = `TRUE`.
`set.par`	Logical indicating whether or not options to par should be set by the function.
`...`	Additional arguments passed along to plot.

plot of residual absorbance values after pre-processing. The lefthand plot is for the model that does not account for the heteroschedastic variance whereas the model for the righthand plot does.

The function was written at department of haematology, Aalborg University Hospital and maintained by Steffen Falgreen.

Steffen Falgreen et al. Exposure time independent summary statistics for assessment of drug dependent cell line growth inhibition (2013)

plotbgModel

require(DoseR)
data(A.data)

## Plot of the drug specific Absorbance measures with an 95% confidence interval.
plotdrugColorCorrection(A.data=A.data, type.plot = c("output"))

## Plot of the absorbance values. Use this plot for dagnostics of each dose response 
## experiment. Plates that are not fitted adequately should be removed a plate is found 
## In the plot to the left, the raw data is shown, the middle plot shows the absorbance values
## corrected in the conventional way, and the right plot shows the model corrected absorbance values.

par(mfrow = c(2,3))
plotdrugColorCorrection(A.data    = A.data, 
                        drugs     = "Doxorubicin",
                        set.par   = FALSE,
                        type.plot = c("raw"))
    
plotdrugColorCorrection(A.data    = A.data, 
                        drugs     = "Rituximab",
                        set.par   = FALSE,
                        type.plot = c("raw"))