qpcR (version 1.1-8)

pcrplot: Plotting PCR data with fitted curves

Description

Displays fitted curves and observations in the same plot window, distinguishing between curves by different plot symbols and line types. Various additional features can be plotted, i.e. error bars or confidence bands.

Usage

pcrplot(x, ..., level = NULL, col = FALSE, 
       conLevel, conName, grid = 100, legend, legendText, legendPos,
       type = "average", lty, log = "", pch, xlab, ylab, xlim, ylim, 
       xt = NULL, xtlab = NULL, yt = NULL, ytlab = NULL,
       add = FALSE, confband = NULL)

Arguments

x

an object of class 'drc'.

...

additional arguments.

level

vector of character strings. To plot only the curves specified by their names.

col

either logical or a vector of colours. If TRUE default colours are used. If FALSE (default) no colours are used.

conLevel

numeric. Dose level below which the dose is zero (the amount of stretching on the x-axis above zero). Default is 1e-2.

conName

character string. Name on x axis for dose zero. Default is '"0"'.

grid

numeric. Number of points in the grid used for plotting the fitted curves.

legend

logical. If TRUE a legend is displayed.

legendText

a character string or vector of character strings specifying the legend text.

legendPos

numeric vector of length 2 giving the position of the legend.

type

a character string specifying how the originals observations should be plotted. There are 5 options: "average" (default), "none" (only the fitted curve(s)), "obs" (only the data points), "all" or "points" (all data point

lty

a numeric vector specifying the line types.

log

a character string which contains '"x"' if the x axis is to be logarithmic, '"y"' if the y axis is to be logarithmic and '"xy"' or '"yx"' if both axes are to be logarithmic. The default is "", which yields the original axe

pch

a vector of plotting characters or symbols.

xlab

an optional label for the x axis.

ylab

an optional label for the y axis.

xlim

a numeric vector of length two, containing the lower and upper limit for the x axis.

ylim

a numeric vector of length two, containing the lower and upper limit for the y axis.

xt

a numeric vector containing the positions of the tick marks on the x axis.

xtlab

a vector containing the tick marks on the x axis.

yt

a numeric vector containing the positions of the tick marks on the y axis.

ytlab

a vector containing the tick marks on the y axis.

add

logical. If TRUE then add to already existing plot.

confband

numeric. The confidence level.

Value

• An invisible data frame with the values used for plotting the fitted curves. The first column contains the PCR cycles, and the following columns (one for each curve) contain the fitted fluorescence data.

Details

Is an extension of the plot.drc function from the 'drc' package.

Examples

repData <- repform(reps[,1:5], c(0,1,1,1,1))
m <- drmfit(values ~ Cycles, curve = Curve, data = repData, fct = l5())
###plot the average
pcrplot(m)
###all observations
pcrplot(m, type = "all")
###mean with errorbars
pcrplot(m, type = "errbar")
###plot one curve and add 95 percent confidence band
m2 <- drmfit(F1.1 ~ Cycles, data = reps, fct = l5())
pcrplot(m2, confband = 0.95)