Snapshot-class {ShortRead} | R Documentation

## Class `"Snapshot"`

### Description

A `Snapshot`-class to visualize genomic data from BAM files with zoom and pan functionality.

### Usage

    Snapshot(files, range, ...)

### Arguments

`files` | A character() or `BamFileList` specifying the file(s) to be visualized.
`range` | A `GRanges` object specifying the range to be visualized.
`...` | Additional, optional, arguments to be passed to the Snapshot `initialize` function. Arguments include: functions: A `SnapshotFunctionList` of functions, in addition to built-in ‘fine_coverage’, ‘coarse_coverage’, ‘multifine_coverage’, to be used for visualization. currentFunction: character(1) naming the function, from `functions` to be used for data input and visualization. The default chooses a function based on the scale at which the data is being visualized. annTrack: Annotation track. If built-in visualization functions are to be used, `annTrack` should be a `GRanges` instance and the first column of its elementMeatdata would be used to annotate the range. fac: Character(1) indicating which factor used for grouping the sample files. The factor should be included in the elementMetadata of `files`, otherwise ignored. Used only to visualize multiple files. .auto_display: logical(1) indicating whether the visualization is to be updated when `show` is invoked. .debug logical(1) indicating whether debug messages are to be printed.

### Methods

zoom

  `signature(x = "Snapshot")`: Zoom (in or out) the current plot.

pan

  `signature(x = "Snapshot")`: Pan (right or left) the current plot.

togglefun

  `signature(x = "Snapshot")`: Toggle the current functions which imported records are to be immediately evaluated. Note that the active range will be changed to the current active window.

togglep

  `signature(x = "Snapshot")`: Toggle the panning effects.

togglez

  `signature(x = "Snapshot")`: Toggle the zooming effects.

### Accessors

show

  `signature(object = "Snapshot")`: Display a `Snapshot` object.

files

  `signature(x = "Snapshot")`: Get the `files` field (object of class `BamFileList`) of a `Snapshot` object.

functions

  `signature(x = "Snapshot")`: Get the `functions` field (object of `SnapshotFunctionList`) of a `Snapshot` object.

view

  `signature(x = "Snapshot")`: Get the `view` field (object of `SpTrellis`) of a `Snapshot` object.

vrange

  `signature(x = "Snapshot")`: Get the `.range` field (object of `GRanges`) of a `Snapshot` object.

getTrellis

  `signature(x = "Snapshot")`: Get the `trellis` object, a field of the `SpTrellis` object.

### Fields

`.debug`:

  Object of class `function` to display messages while in debug mode

`.auto_display`:

  Object of class `logical` to automatically display the coverage plot.

`.range`:

  Object of class `GRanges` indicating which ranges of records to be imported from BAM fields.

`.zin`:

  Object of class `logical` indicating whether the current zooming effect is zoom in.

`.pright`:

  Object of class `logical` indicating whether the current panning effect is right.

`.data`:

  Object of class `data.frame` containing coverage a position is represented for each strand and BAM file.

`.data_dirty`:

  Object of class `logical` indicating whether to re-evaluate the imported records.

`.initial_functions`:

  Object of class `SnapshotFunctionList` available by the `Snapshot` object.

`.current_function`:

  Object of class `character` of the function the imported recorded are currently evaluated and visualized.

`annTrack`:

  Default to `NULL` if not intended to visualize the annotation track. If default visualization function(s) is intended to be used to plot the annotation, `annTrack` has to be a `GRanges` instance.

`functions`:

  Object of class `SnapshotFunctionList` of customized functions to evaluate and visualize the imported records.

`files`:

  Object of class `BamFileList` to be imported.

`view`:

  Object of class `SpTrellis` that is essentially a reference class wrapper of `Trellis` objects.

### Class-Based Methods

`display()`:

  Display the current `Snapshot` object.

`pan()`:

  Pan (right or left) the current plot.

`zoom()`:

  Zoom (in or out) the current plot.

`toggle(zoom, pan, currentFunction)`:

  Toggle zooming, panning effects or the currentFuction in which the imported records are to be evaluated and visualized.

### Author(s)

Martin Morgan and Chao-Jen Wong cwon2@fhcrc.org

### See Also

`SpTrellis`

### Examples

    ## example 1: Importing specific ranges of records

    file <- system.file("extdata", "SRR002051.chrI-V.bam",
                        package="yeastNagalakshmi")
    which <-  GRanges("chrI", IRanges(1, 2e5))
    s <- Snapshot(file, range=which)

    ## methods
    zoom(s) # zoom in
    ## zoom in to a specific region
    zoom(s, range=GRanges("chrI", IRanges(7e4, 7e4+8000)))
    pan(s)  # pan right
    togglez(s) # change effect of zooming
    zoom(s) # zoom out
    togglep(s) # change effect of panning
    pan(s)

    ## accessors
    functions(s)
    vrange(s)
    show(s)
    ignore.strand(s)
    view(s) ## extract the spTrellis object
    getTrellis(s) ## extract the trellis object

    ## example 2: ignore strand
    s <- Snapshot(file, range=which, ignore.strand=TRUE)

    ##
    ## example 3: visualizing annotation track
    ##

    library(GenomicFeatures)

    getAnnGR <- function(txdb, which) {
        ex <- exonsBy(txdb, by="gene")
        seqlevels(ex, pruning.mode="coarse") <- seqlevels(which)
        r <- range(ex)
        gr <- unlist(r)
        values(gr)[["gene_id"]] <- rep.int(names(r), times=lengths(r))
        gr
    }

    txdbFile <- system.file("extdata", "sacCer2_sgdGene.sqlite",
                        package="yeastNagalakshmi")
    # txdb <- makeTxDbFromUCSC(genome="sacCer2", tablename="sgdGene")
    txdb <- loadDb(txdbFile)
    which <-  GRanges("chrI", IRanges(1, 2e5))
    gr <- getAnnGR(txdb, which)
    ## note that the first column of the elementMetadata annotates of the
    ## range of the elements.
    gr

    s <- Snapshot(file, range=which, annTrack=gr)
    annTrack(s)
    ## zoom in to an interesting region
    zoom(s, range=GRanges("chrI", IRanges(7e4, 7e4+8000)))

    togglez(s) ## zoom out
    zoom(s)

    pan(s)

    ## example 4, 5, 6: multiple BAM files with 'multicoarse_covarage'
    ## and 'multifine_coverage' view.

    ## Resolution does not automatically switch for views of multiple
    ## files. It is important to note if width(which) < 10,000, use
    ## multifine_coverage.  Otherwise use multicoarse_coverage
    file <- system.file("extdata", "SRR002051.chrI-V.bam",
                        package="yeastNagalakshmi")
    which <-  GRanges("chrI", IRanges(1, 2e5))
    s <- Snapshot(c(file, file), range=which,
                  currentFunction="multicoarse_coverage")

    ## grouping files and view by 'multicoarse_coverage'
    bfiles <- BamFileList(c(a=file, b=file))
    values(bfiles) <- DataFrame(sampleGroup=factor(c("normal", "tumor")))
    values(bfiles)
    s <- Snapshot(bfiles, range=which,
                  currentFunction="multicoarse_coverage", fac="sampleGroup")

    ## grouping files and view by 'multifine_coverage'
    which <- GRanges("chrI", IRanges(7e4, 7e4+8000))
    s <- Snapshot(bfiles, range=which,
                  currentFunction="multifine_coverage", fac="sampleGroup")

[Package ShortRead version 1.38.0 Index]