## 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 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.
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)
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.
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(.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)
An alternative to gridsvgjs() that allows the user to tweak ggplot parameters within the browser application itself.
gridtweak()
A pared-down, stand-alone force network shiny app for any dataframe.
simplenet(mtcars)
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