Description Usage Arguments Value Author(s) References See Also Examples
View source: R/plotfunctions.R
This function is used to test that the fit of the normalisation model is adequate and that the heteroschedastic variance is fitted correctly.
1 2 3 4 |
A.data |
An A.data object created by either the function |
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 |
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. |
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)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | 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)
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