.atrack
is an S4 generic method that converts an
object into an annotation track object. It provides a
general and flexible annotation framework that is used by
aheatmap
to annotates heatmap rows and
columns.
is.atrack
tests if an object is an
annotationTrack
object.
adata
get/sets the annotation parameters on an
object
amargin
get/sets the annotation margin, i.e. along
which dimension of the data the annotations are to be
considered.
anames
returns the reference margin names for
annotation tracks, from their embedded annotation data
object.
alength
returns the reference length for
annotation tracks, from their embedded annotation data
object
atrack
creates/concatenates annotationTrack
objects
annotationTrack
is constructor function for
annotationTrack
object
.atrack(object, ...) is.atrack(x)
adata(x, value, ...)
amargin(x, value)
anames(x, default.margin)
alength(x, default.margin)
# S4 method for ANY
.atrack(object, data = NULL, ...)
atrack(..., order = NULL, enforceNames = FALSE,
.SPECIAL = NA, .DATA = NULL, .CACHE = NULL)
annotationTrack(x = list())
atrack
returns a list, decorated with class
'annotationTrack'
, where each element contains the
description of an annotation track.
an object from which is extracted annotation tracks
extra arguments to allow extensions and passed
to the next method call. For atrack
, arguments in
...
are concatenated into a single
annotationTrack
object.
an R object
replacement value for the complete annotation data list
margin to use if no margin data is
stored in the x
.
object used to extend the annotation track
within a given data context. It is typically a
matrix-like object, against which annotation
specifications are matched using
match_atrack
.
an integer vector that indicates the order of the annotation tracks in the result list
logical that indicates if missing
track names should be generated as X<i>
an optional list of functions (with no
arguments) that are called to generate special annotation
tracks defined by codes of the form ':NAME'
. e.g.,
the function link{consensusmap}
defines special
tracks ':basis'
and ':consensus'
.
If .SPECIAL=FALSE
, then any special tracks is
discarded and a warning is thrown.
data used to match and extend annotation
specifications. It is passed to argument data
of
the .atrack
methods, which in turn use pass it to
match_atrack
.
an annotationTrack
object with which
the generated annotation track should be consistent. This
argument is more for internal/advanced usage and should
not be used by the end-user.
signature(object = "ANY")
: The
default method converts character or integer vectors into
factors. Numeric vectors, factors, a single NA or
annotationTrack
objects are returned unchanged
(except from reordering by argument order
). Data
frames are not changed either, but class
'annotationTrack' is appended to their original class
set.
Methods for .atrack
exist for common type of
objects, which should provide enough options for new
methods to define how annotation track are extracted from
more complex objects, by coercing/filtering them into a
supported type.