R: Annotation Tracks

.atrack {NMF} | R Documentation

## Annotation Tracks

### Description

`.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

### Usage

      .atrack(object, ...)

      is.atrack(x)

      adata(x, value, ...)

      amargin(x, value)

      anames(x, default.margin)

      alength(x, default.margin)

      ## S4 method for signature 'ANY'
    .atrack(object, data = NULL, ...)

      atrack(..., order = NULL, enforceNames = FALSE,
        .SPECIAL = NA, .DATA = NULL, .CACHE = NULL)

      annotationTrack(x = list())

### Arguments

`object` | 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.
`x` | an R object
`value` | replacement value for the complete annotation data list
`default.margin` | margin to use if no margin data is stored in the `x`.
`data` | 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`.
`order` | an integer vector that indicates the order of the annotation tracks in the result list
`enforceNames` | logical that indicates if missing track names should be generated as `X<i>`
`.SPECIAL` | 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` | 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`.
`.CACHE` | 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.

### Details

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.

### Value

`atrack` returns a list, decorated with class `'annotationTrack'`, where each element contains the description of an annotation track.

### Methods

.atrack

  `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.

[Package NMF version 0.21.0 Index]