## 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
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
draw an SummarizedExperiment object
draw a GRanges object
draw a GRangesList object
draw an ExpressionSet object
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.
An alternative to gridsvgjs() that allows the user to tweak ggplot parameters within the browser application itself.
A pared-down, stand-alone force network shiny app for any dataframe.
Joe Cheng and Winston Chang
Help with the display method for data.frames