bicgo: Open a Shiny Application for manual/interactive biclustering and GO exploration

Description

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

Usage

bicgo(object, ...)

Arguments

Value

Any ExpressionSet object.

See Also

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

Examples

if(interactive()) {

## Open an browser application for the purpose of manually biclustering an  
## ExpressionSet object and obtaining a GO summary for a specific bicluster.

data(expr)
bicgo(expr)

}

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/bicgo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bicgo
> ### Title: bicgo: Open a Shiny Application for manual/interactive
> ###   biclustering and GO exploration
> ### Aliases: bicgo bicgo,ANY-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> #if(interactive()) {
> 
> ## Open an browser application for the purpose of manually biclustering an  
> ## ExpressionSet object and obtaining a GO summary for a specific bicluster.
> 
> data(expr)
> bicgo(expr)
Loading required package: shiny
Loading required package: GOstats
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: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: graph


Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph

Loading required package: GO.db
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: mixOmics
Loading required package: MASS

Attaching package: 'MASS'

The following object is masked from 'package:AnnotationDbi':

    select

Loading required package: lattice
Loading required package: ggplot2

Loaded mixOmics 6.0.0

Visit http://www.mixOmics.org for more details about our methods.
Any bug reports or comments? Notify us at mixomics at math.univ-toulouse.fr or https://bitbucket.org/klecao/package-mixomics/issues

Thank you for using mixOmics!
Error in loadNamespace(name) : 
  there is no package called '.interactiveDisplayBase'
Calls: bicgo ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted