## Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.

interactiveDisplay

interactiveDisplay uses the function display() to host a browser based application on the fly using the Shiny package. Currently 4 Bioconductor objects: Granges, GrangesList, ExpressionSet and SummarizedExperiment are supported with tailored methods. In some cases, grid based plots are converted to SVG with the gridSVG package and additional JavaScript is appended for simple mousewheel zoom and panning. Shiny UI elements are available based on the object passed to display(). These allow the user to modify how the plot is displayed, and for some objects, modify or subset the data and send it back to the console.

Methods

draw an SummarizedExperiment object

data(se)
display(se)

draw a GRanges object

data(mmgr)
display(mmgr)

draw a GRangesList object

data(mmgrl)
display(mmgrl)

draw an ExpressionSet object

data(expr)
display(expr)

subsetting

Many of the display method will have a button that allows you return subset values back to the R session. To use these, couple the intial call with an assignment operator like this:

mtcars2 <- display(mtcars)

Once you leave the diplay web gui, the results of the above interaction will be captured inside of mtcars2.

Additional Functionality

In addition to the main display() function, the user can send any grid based plot to the browser as a JS interactive SVG.

library(ggplot2)
data(mtcars)
qp <- qplot(mpg, data = mtcars, geom = "density", fill = factor(cyl), alpha = I(0.4))
gridsvgjs(qp)

There is an simplified, alternative (work-in-progress) function for ExpressionSet objects for the purpose of manually selecting a bicluster and obtaining a GO summary.

data(expr)
bicgo(expr)

Acknowledgments

Shiny
Joe Cheng and Winston Chang
http://www.rstudio.com/shiny/

Force Layout
Jeff Allen
https://github.com/trestletech/shiny-sandbox/tree/master/grn

gridSVG
Simon Potter
http://sjp.co.nz/projects/gridsvg/

Zoom/Pan JavaScript libraries
John Krauss
https://github.com/talos/jquery-svgpan
Andrea Leofreddi
https://code.google.com/p/svgpan/

JavaScript Color Chooser
Jan Odvarko
http://jscolor.com/

Data-Driven Documents
Michael Bostock
http://d3js.org/

Javascript for returning values from data.frames
Kirill Savin

Help with the display method for data.frames
Dan Tenenbaum