update.TRAMP {TRAMPR} | R Documentation |
This function allows some manual checking and correction of
a TRAMP
object. By default, it steps through each
sample, and offers to (1) add a new known to the
TRAMPknowns
database within the TRAMP
object (see
add.known
for details), (2) mark matches to be ignored
in future calls to plot.TRAMP
(see
remove.TRAMP.match
), (3) save the current plot as a
PDF.
## S3 method for class 'TRAMP': update(object, sample.fk=labels(object$samples), grouped=FALSE, ignore=TRUE, delay.rebuild=FALSE, default.species=NULL, filename.fmt="TRAMP_%d.pdf", ...)
object |
A TRAMP object. |
sample.fk |
A vector of sample.fk to cycle through. If
omitted, this will default to all samples present in the
TRAMPsamples component of the TRAMP object. |
grouped, ignore |
Plotting parameters, as in
plot.TRAMP . Currently these cannot be altered from
their default values. |
delay.rebuild |
Logical: Should the rebuild of the TRAMP
object be delayed until the function returns? If this is
FALSE (the default), then the TRAMP object will
rebuild every time a new known is added. This may take a while for
large objects, so if set to TRUE , then the TRAMP
object will not be rebuilt until all sample.fk s have been
displayed. This means that any new samples added as knowns will not
be included in plots. |
default.species |
Default species name for newly added knowns.
Passed to add.known . |
filename.fmt |
Format used to generate filenames when saving
PDFs. Include a "%d" to stand in for the sample.fk
(so "TRAMP_%d.pdf" becomes "TRAMP_12.pdf" for
sample.fk 12). |
... |
Further arguments passed to the plotting function
plot.TRAMP . |
If an error occurs while running update
, all modifications will
be lost.
update.TRAMP
returns a modified TRAMP
object, and does
not modify the original TRAMP
object in place. You must use it
like:
x <- update(x)
or
x2 <- update(x)
to modify the original object or create a new, modified object in
place. Note that if creating mutiple objects, if the
TRAMPknowns
object has a file.pat
element, then
any changes to either of x
or x2
will be written back to
file, but the knowns contained in x
and x2
may be
different. See the note in add.known
.
The action “Quit” will always exit the update
function and
save the object.
Be careful when using a TRAMP
object whose TRAMPknowns
element has a file.pat
element; new knowns added will be
immediately written to file.
## Since this function runs interactively, there can be no sample.