qpcR (version 1.2-4)

plot.pcrfit: Plotting qPCR data with fitted curves/confidence bands/error bars

Description

A plotting function for data of class 'pcrfit' (single curves), 'modlist' (batch curves) or 'replist' (replicate curves) displaying the data points, the fitted curve and (if desired) confidence/prediction bands/error bars on replicates. Three different plot types are available, namely plotting all curves in 2D/3D graphs or a plot matrix with one graph per curve.

Usage

## S3 method for class 'pcrfit':
plot(x, fitted = TRUE,  
        confband = c("none", "confidence", "prediction"),
        errbar = c("none", "sd", "se", "conf"), add = FALSE, 
        col = NULL, level = 0.95, xlim = NULL, 
        which = c("all", "single", "3D"), ...)

Arguments

x

an object of class 'pcrfit', 'modlist' or 'replist'.

fitted

should the fitted line be displayed?

confband

should confidence/prediction bands be displayed? See confint.

errbar

the type of error bar on the plot if replicates exist. See 'Examples'.

add

should the curve be added to an existing plot?

col

an optional color vector for the individual curves. Is recycled to the number of runs in x.

level

the confidence level used for confband or errbar.

xlim

a 2-element vector of the x-value (Cycles) region that should be plotted.

which

plots all curves in one 2D or 3D graph or many graphs with single curves.

...

other parameters to be passed to plot or predict.

Value

• A qPCR plot. If object was of class 'replist', colour coding of the curves is done automatically.

Details

Uses the 'rgl' package for 3D plots. If the 'modlist' contains data that failed to fit, these are missing in the plots.

Examples

## single plot
m1 <- pcrfit(reps, 1, 2, l5)
plot(m1)

## add another plot in blue
## with 99\% confidence interval
m2 <- pcrfit(reps, 1, 12, l5)
plot(m2, add = TRUE, col = 4, confband = "confidence", level = 0.99)

## plot a 'modlist' batch with coloring of replicates
ml <- modlist(reps, 1, 2:13, model = l4)
plot(ml, col = gl(3,4))   

## only the fitted curves
## and a subset of data
plot(ml, type = "n", col = gl(3,4), xlim = c(10, 30))

## plot a 'replist'
rl <- replist(ml, group = gl(3, 4))
plot(rl)

## standard deviation instead of 
## replicate points
plot(rl, type = "n", errbar = "sd")
## 95\% confidence values
plot(rl, type = "n", errbar = "conf")

## plot single curves.
## good for diagnostics...
plot(ml, which = "single", col = gl(3, 4))

## 3D plots of 'modlist's or 'replist's
plot(ml, which = "3D", col = gl(3, 4))
rgl.close()
plot(rl, which = "3D")
rgl.close()