plot-bg: Plot 'bg' objects

In chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data

Description

Draws diagnostic plots of amplification reaction.

Usage

## S4 method for signature 'bg'
plot(x, what = 1:3, add = FALSE, indicators = TRUE, 
		    legend = TRUE, stan.labs = TRUE, 
		    plot.colors = c("black", "red", "blue"), ...)

Arguments

x	is a bg object.
what	is a vector specifying what should be plotted. 1 means raw data, 2 means first derivative and 3 means second derivative. Any combination of mentioned values is valid, for example: c(1,2), c(1, 2, 3), c(2, 3). See Details and Examples.
add	is a "logical" argument. If TRUE, plot is added to existing plot. Moreover, enforces indicators = FALSE.
indicators	is a "logical" argument. If FALSE, background start, stop and plateau transition indication lines aren't plotted.
legend	is a "logical" argument. If TRUE, legend is added to the plot.
stan.labs	is a "logical" argument. If TRUE, standard axis labels ("Cycle" and "Fluorescence") are added.
plot.colors	is a vectors of colors used in plot. Must have length 3.
...	Arguments to be passed further to the plot function, such as graphical parameters.

Details

plot.bg is simplified, ready-to-use version of plot.der, which still can be used whenever more flexible function is needed.

Author(s)

Stefan Roediger, Michal Burdukiewicz

See Also

bg, plot.der

Examples

#step-by-step plotting bg object

res <- AmpSim(cyc = 1:40, Cq = 25)
background <- bg.max(res)

plot(background)

#above is equivalent of below
plot(rounder(inder(res)), xlab = "Cycles", 
     ylab = "Fluorescence",
     pch = 20, legend = FALSE)

abline(v = slot(background, "bg.start"))
  text(slot(background, "bg.start"), 0.2, "Background start", pos = 4)
abline(v = slot(background, "bg.stop"), col = "blue")
  text(slot(background, "bg.stop"), 0.25, "Background stop", pos = 4, 
       col = "blue")
abline(v = slot(background, "amp.stop"), col = "green")
  text(slot(background, "amp.stop"), 0.3, "Plateau transition", pos = 4, 
       col = "green")
legend(4, 1, c("Raw data", "First derivative", "Second derivative"), 
       pch = rep(20, 3), col = c(1, 2, 4))

chipPCR documentation built on March 5, 2021, 9:06 a.m.