Introduction to epivizrStandalone

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. You can find more information about Epiviz at http://epiviz.cbcb.umd.edu/help and see a video tour here.

This package, epivizrStandalone, makes it possible to run the web app UI locally completely within R. The epivizr package implements two-way communication between the R/Bioconductor computational genomics environment and Epiviz. Objects in an R session can be displayed as tracks or plots on Epiviz. Epivizr uses Websockets for communication between the browser Javascript client and the R environmen, the same technology underlying the popular Shiny system for authoring interactive web-based reports in R. See the epivizr package vignette for more information on how to interact with the epiviz JS app.

Running the epiviz visualization app as a standalone allows it to browse any genome of interest using Bioconductor infrastructure. For example, to browse the mouse genome we would do the following.

library(epivizrStandalone)
library(Mus.musculus)

app <- startStandalone(Mus.musculus, keep_seqlevels=paste0("chr",c(1:19,"X","Y")), verbose=TRUE, use_viewer_option = TRUE)  

library(epivizrStandalone)
library(Mus.musculus)

app <- startStandaloneApp(Mus.musculus, keep_seqlevels=paste0("chr",c(1:19,"X","Y")), verbose=TRUE) 

app$stop_app()