addScheme(scheme, name)getScheme(name=getOption("Gviz.scheme"))
dp slot from the
GdObject DisplayPars plotTracks function. In both cases, all
additional arguments that are not caught by any of the formally
defined function parameters are being interpreted as additional
display parameters and are automatically added to the aforementioned
slot. The main difference here is that display parameters that are
passed on to the constructor function are specific for an individual
track object, whereas those supplied to the plotTracks function
will be applied to all the objects in the plotting list. Not all
display parameters have an effect on the plotting of all track
classes, and those will be silently ignored.
One can query the available display parameters for a given class as
well as their default values by calling the
availableDisplayPars function, or by inspecting the man
pages of the individual track classes. The structure of the classes
defined in this package is hierarchical, and so are the available
display parameters, i.e., all objects inherit the parameters defined
in the commom GdObject parent class, and so on.
Once a track object has been created, the display parameters are still
open for modification. To this end, the displayPars
replacement method is available for all objects inheriting from class
GdObject. The method takes a named list of parameters as input,
e.g.:
displayPars(foo) <- list(col="red", lwd=2)
In the same spirit, the currently set display parameters for the
object foo can be inferred using the displayPars method
directly, e.g.:
displayPars(foo)
For track objects inheriting from class
AnnotationTrack feature
argument. For most of the tracks that have been inferred from one of
the online repositories, this classification will usually be
downloaded along with the actual annotation data. Users might find themselves changing the same parameters over and over
again, and it would make sense to register these modifications in a
central location once and for all. To this end the Gviz package
supports display parameter schemes. A scheme is essentially just a
bunch of nested named lists, where the names on the first level of
nesting should correspond to track class names, and the names on the
second level to the display parameters to set. The currently active
schmeme can be changed by setting the global option
Gviz.scheme, and a new scheme can be registered by using the
addScheme function, providing both the list and the name for
the new scheme. The getScheme function is useful to get the
current scheme as a list structure, for instance to use as a skeleton
for your own custom scheme.
In order to make these settings persitant across R sessions one can
create one or several schemes in the global environment in the special
object .GvizSchemes, for instance by putting the necessary code
in the .Rprofile file. This object needs to be a named list of
schemes, and it will be collected when the Givz package loads. Its
content is then automatically added to the collection of available
schemes.
Please note that because display parameters are stored with the track
objects, a scheme change only has an effect on those objects that are
created after the change has taken place.
AnnotationTrack