display: Open a Shiny application for a Bioconductor object

Description

This opens a shiny visualization application in the browser based on the submitted object.

Usage

display(object, ...)

Arguments

Value

Usually some variation of the initial input object, but it may be altered by the display widget (subset for example).

Author(s)

Shawn Balcome and Marc Carlson

See Also

http://bioconductor.org/packages/2.13/bioc/html/interactiveDisplay.html

Examples

if(interactive()) {

## draw a RangedSummarizedExperiment object
data(se)
display(se)

## draw a GRanges object
data(mmgr)
display(mmgr)

## some display methods allow subsetting.
## To take advantage, just use an assignment operator like this:
mmgr2 <- display(mmgr)


## draw a GRangesList object
data(mmgrl)
display(mmgrl)

## draw an ExpressionSet object
data(expr)
display(expr)

## draw an MRexperiment object (placeholder!!!)
data(mr)
display(mr)

}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(interactiveDisplay)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/interactiveDisplay/interactiveDisplay-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: display
> ### Title: display: Open a Shiny application for a Bioconductor object
> ### Aliases: display display,ANY-method display,missing-method
> ###   display,ExpressionSet-method display,GRanges-method
> ###   display,GRangesList-method display,RangedSummarizedExperiment-method
> ###   display,MRexperiment-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> #if(interactive()) {
> 
> ## draw a RangedSummarizedExperiment object
> data(se)
> display(se)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: shiny

Listening on http://127.0.0.1:4327