plot.TRAMPsamples {TRAMPR} | R Documentation |
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 class '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 |
sample.fk |
The |
all.samples.global |
Logical: Should plots be set up for all
enzyme/primer combinations present in |
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.
|
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
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()
## End(Not run)