qpcR (version 1.2-2)

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.

Usage

## S3 method for class 'pcrfit':
plot(x, fitted = TRUE, subset = NULL, 
        confband = c("none", "confidence", "prediction"),
        errbar = c("none", "sd", "se", "conf"), add = FALSE, 
        colvec = NULL, level = 0.95, ...)

Arguments

x

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

fitted

should the fitted line be displayed?

subset

a 2-element vector analog to xlim of the data that should be plotted.

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?

colvec

an optional color vector for the individual curves.

level

the confidence level used for confband or errbar.

...

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.

Examples

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

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

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

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

## plot a 'replist'
ml <- modlist(reps, 1, 2:9, model = l4)
rl <- replist(ml, group = gl(2, 4))
plot(rl)

## standard deviation instead of 
## replicate points
plot(rl, type = "none", errbar = "sd")