## ----include=FALSE-------------------------------------------------------
library(knitr)
opts_chunk$set(concordance=TRUE)

## ----install1, eval=FALSE, results='asis'--------------------------------
## source("http://bioconductor.org/biocLite.R")
## biocLite("interactiveDisplay")

## ----install2, eval=FALSE, results='asis'--------------------------------
## source("http://bioconductor.org/biocLite.R")
## useDevel(TRUE)
## biocLite("interactiveDisplay")

## ----citation, eval=TRUE, results='tex'----------------------------------
citation("interactiveDisplay")

## ----libraries, eval=TRUE, results='asis'--------------------------------
options(width=80)
options(continue=" ")
suppressMessages(library(ggplot2))
suppressMessages(library(interactiveDisplay))
suppressMessages(library(Biobase))

## ----data_mmgr, eval=TRUE, results='tex'---------------------------------
data(mmgr)
mmgr

## ----grl, eval=TRUE, results='tex'---------------------------------------
grl <- GenomicRangesList(list(mmgr,mmgr))

## ----data_mmgrl, eval=TRUE, results='tex'--------------------------------
data(mmgrl)
mmgrl

## ----display_mmgr, eval=FALSE, results='asis'----------------------------
## display(mmgr)

## ----display_mmgrl, eval=FALSE, results='asis'---------------------------
## display(mmgrl)

## ----display_mmgr2, eval=FALSE, results='asis'---------------------------
## new_mmgr <- display(mmgr)

## ----display_mmgrl2, eval=FALSE, results='asis'--------------------------
## new_mmgrl <- display(mmgrl)

## ----data_expr, eval=TRUE, results='tex'---------------------------------
data(expr)
expr

## ----exprs_expr, eval=TRUE, results='tex'--------------------------------
exprs(expr)[1:10,1:7]

## ----display_expr, eval=FALSE, results='asis'----------------------------
## display(expr)

## ----data_se, eval=TRUE, results='tex'-----------------------------------
data(se)
se

## ----display_se, eval=FALSE, results='asis'------------------------------
## display(se)

## ----display_mtcars, eval=FALSE, results='asis'--------------------------
## display(mtcars)

## ----display_mtcars2, eval=FALSE, results='asis'-------------------------
## new_mtcars <- display(mtcars)

## ----simplenet_mtcars, eval=FALSE, results='asis'------------------------
## simplenet(mtcars)

## ----plot_mtcars, eval=FALSE, results='asis'-----------------------------
## data(mtcars)
## qp <- qplot(mpg, data=mtcars, geom="density", fill=factor(cyl), alpha=I(.4))
## plot(qp)

## ----gridsvgjs_qp, eval=FALSE, results='asis'----------------------------
## gridsvgjs(qp)

## ----sessionInfo, eval=TRUE, results='tex'-------------------------------
sessionInfo()