TRAMPR (version 1.0-10)

plot.TRAMPsamples: Plot a TRAMPsamples Object

Description

Shows the peak profiles of samples in a TRAMPsamples object, showing the locations and heights of peaks for individual enzyme/primer combinations. This is the same information that is displayed in the bottom portion of a plot.TRAMP plot, but may be useful where a TRAMP fit has not been performed yet (e.g. before a knowns database has been constructed).

Usage

# S3 method for TRAMPsamples
plot(x, sample.fk, ...)
TRAMPsamples.plotone(x, sample.fk, all.samples.global=FALSE, col=1:10,
                     xmax=NULL, mar.default=.5, mar.labels=8, cex=1)

Arguments

x

A TRAMPsamples object, containing profiles to plot.

sample.fk

The sample.fk to plot. If omitted, then all samples are plotted, one after the other (this is useful for generating a summary of all fits for printing out: see Example).

all.samples.global

Logical: Should plots be set up for all enzyme/primer combinations present in x, even if the combinations are not present for all individual cases? Analagous to the same argument in plot.TRAMP. (This is useful for keeping combinations in the same place, and plotted with the same colours.)

col

Vector of colours to plot the different enzyme/primer combinations. There must be at least as many colours as there are different combinations.

xmax

Maximum size (in base pairs) for the plots to cover. NULL (the default) uses the range of all data found in the TRAMPsamples object (rounded up to the nearest 100). NA will use the range of all data in the current sample.

mar.default

Margin size (in lines of text) to surround the plot.

mar.labels

Number of lines of text to be used for labels to the left of the plots. Increase this if labels are being truncated.

cex

Scaling factor for text.

...

Additional arguments (ignored).

See Also

plot.TRAMP, the plotting method for TRAMP objects, and plot.TRAMPknowns, for TRAMPknowns objects.

Examples

# NOT RUN {
data(demo.samples)

plot(demo.samples, 101)
plot(demo.samples, 117)

# }
# NOT RUN {
# Create a PDF file with all profiles:
pdf("all_profiles.pdf")
plot(demo.samples)
dev.off()
# }