plotbgModelresid: Function for plotting the residuals of the fitted absorbance...

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

View source: R/plotfunctions.R

Description

This function is used to test that the fit of the normalisation model is adequate and that the heteroschedastic variance is fitted correctly.

Usage

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plotbgModelresid(A.data, names = NULL, times = NULL, drugs = NULL, 
                  pdfit = FALSE, file = file.path(getwd(), "resid.plots.pdf"), 
                  pointsize = 12, xlab = "Fitted values", ylab = "Residuals", 
                  main = NULL, col = 1:8, width = 3.34, height = 2.23097112)

Arguments

A.data

An A.data object created by either the function bgModel.

names

Character vector with the names of the cell lines for which the plot should be made. Defeaults to NULL where a plot is generated for all cell lines.

times

Numeric vector with the time.points for which the plot should be made. Defeaults to NULL where a plot is generated for all time points.

drugs

Character vector with the drugs for which the plot should be made. Defeaults to NULL where a plot is generated for all drugs.

pdfit

Logical. if TRUE all plots are saved in a pdf with name given in the file argument.

file

Character giving the name of the created pdf file.

pointsize

The pointsize used in the created pdf.

xlab

Character specifying the name for the x-axis.

ylab

Character specifying the name for the x-axis.

main

Character specifying the title for the plot.

col

Vector with colours for each experiment.

width

Numeric value specifying the width of the pdf.

height

Numeric value specifying the width of the pdf.

Value

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.

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

plotbgModel

Examples

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require(DoseR)
data(A.data)

# Plot the residuals to check whether any of the fits are 
# very poor. In order to do the plot for the cell line RPMI-8226 
# at the 48 hour time.point for the drug Doxorubidin the 
# following code is used:

plotbgModelresid(A.data, 
                 names = "RPMI-8226",
                 times = 48,
                 drugs = "Doxorubicin",
                  col = c("#71965A", "#4F6E9F", "#9F9692", "#9D2441",
                         "#333333", "#662D91", "#71DEC0", "#F7931E"))
      
# The following code chunk saves the residual plot for all cell lines,
# all drugs, and all times in the pdf file "resid.plots.pdf".                     
                         
# plotbgModelresid(A.data, names = NULL,
#                 times = NULL,
#                 drugs = NULL,
#                 pdfit = TRUE,
#                 file=  "resid.plots.pdf",
#                 col = c("#71965A", "#4F6E9F", "#9F9692", "#9D2441",
#                         "#333333", "#662D91", "#71DEC0", "#F7931E"),
#                 pointsize = 6,
#                 width = 13/2.54, height =(13/2.54)/1.5)

oncoclass/DoseR documentation built on Nov. 23, 2017, 4:12 a.m.