Description Usage Arguments Value Author(s) Examples
Plots of the "restricted" and "unrestricted" fits for parallel line models. Also plots of the model with individual fits for each combination of sample and dose can be displayed, on the scale of observed values, or corrected for the mean of the values for the dilution step. Finally residuals can be plotted in qq-plots (qqnorm), histograms, box-plots, or against dilutions step, sample, repetition, row, column, block, plate, etc.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | pla.plots(dataframe,
sampleLabels = levels(unlist(dataframe["Sample"])),
indexOfReference = 1,
design = "blocks",
main = "Parallel Line Model",
setPdf = FALSE,
pdfName = "PlaPlots.pdf",
nc = 4,
mfrow = c(2, nc),
oma = c(1, 0, 2, 0),
mar = c(3.5, 3.5, 0, 0) + 0.6,
joinReplicates = TRUE,
showRho = FALSE,
plots = "default",
xlab = "Log(Dosis)",
ylab = "Response: Response",
pch = 14 + as.numeric(unlist(dataframe["Replicate"])),
cex = 2,
lwd = 4,
colTst = "black",
colRef = "grey",
colRho = "grey10",
colNrm = "grey70",
tests = NULL)
|
dataframe |
The data.frame with relevant variables, created by functions data2assayFrame or assayTable2frame - as for pla.fit. |
sampleLabels |
A vector of character strings giving the labels of the |
indexOfReference |
Index of the reference among the samples
given by |
design |
|
main |
Main title for plot. |
setPdf |
If |
pdfName |
A character string giving the name of the file for PDF graphics. |
nc |
|
mfrow |
See par. |
oma |
See par. |
mar |
See par. |
joinReplicates |
See plotSamples. |
showRho |
See plotSamples. |
plots |
A (vector of) character strings from the list "default", "all", "restricted", "unrestricted", "twoway", "stepadjusted", "qplot", "histogram", "residualsSamples", "residualsBoxSampleStep", "residualsBoxSample", "residualsRow", "residuals-Column", "residualsBlock", "residualsPlate", "residualsStep". |
xlab |
See plotSamples. |
ylab |
See plotSamples. |
pch |
See plotSamples. |
cex |
See plotSamples. |
lwd |
See plotSamples. |
colTst |
Color(s) of |
colRef |
Color of |
colRho |
Color of displayed potency. |
colNrm |
Color for qqnorm and curve in histogram. |
tests |
Optional returned values from pla.fit. |
No values returned.
Jens Henrik Badsberg
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 | data(HepatitisB); Data <- HepatitisB
Design <- "crd"
Data <- readAssayTable(paste(system.file(package = "pla"),
"vignettes/PhEur/data/HepatitisB.txt",
sep = "/"))
Frame <- as.data.frame(Data)
fits <- pla.fit(Frame, design = Design, sampleLabels = c("S", "T", "U", "V"),
dr = 2.25, returnPotencyEstimates = TRUE)
cbbPalette <- c("#000000", "#009E73", "#e79f00", "#9ad0f3",
"#0072B2", "#D55E00", "#CC79A7", "#F0E442")
plots <- pla.plots(Frame, sampleLabels = c("S", "T", "U", "V"),
nc = 3, showRho = FALSE, colTst = cbbPalette[2:4],
## main = Data@assayTitle,
main = "PhEur: HepatitisB; Three hepatitis B vaccines against a standard",
tests = fits@tests)
## Alternative on object of class 'pla':
plaModel <- plaCRD(Data,
assayTitle = "PhEur: HepatitisB; Three hepatitis B vaccines against a standard")
print(plaModel, formatTest = "short")
plots <- plot(plaModel)
|
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