In HCBravoLab/bioc2016Addendum: Some changes to make workshop smoother

In this document we setup the starting workspace for the workshop to run locally using the epivizrStandalone package and the Rstudio viewer pane, to make it easier to work with.

The goal is to add a genes track for hg19, a track with CpG islands, and a heatmap with expression from the gene expression barcode project.

Let's start the application with hg19 as the reference for genes track.

library(bioc2016Addendum)
library(epivizrStandalone)
library(Homo.sapiens)

app <- startStandalone(Homo.sapiens, keep_seqlevels=paste0("chr",c(10,11,20)), chr="chr11", use_viewer_option=TRUE, port=7345)

Now, let's add the CpG island track included in this package.

data(cgi_gr)
cgi_track <- app$plot(cgi_gr, datasource_name="CpG Islands")

Now, let's add a heatmap with the gene expression barcode data

data(bcode_eset)
bcode_ms <- app$data_mgr$add_measurements(bcode_eset, "Gene Expression Barcode")
bcode_hmap <- app$chart_mgr$visualize("HeatmapPlot", datasource=bcode_ms)