--- title: "An alternative way of running this workshop exercise" author: "Hector Corrada Bravo" date: "`r Sys.Date()`" output: html_document vignette: > %\VignetteIndexEntry{Vignette Title} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- In this document we setup the starting workspace for the workshop to run locally using the `epivizrChart` 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. lets first load the libraries ```{r, eval=TRUE} library(epivizrChart) library(Homo.sapiens) library(epivizWorkshop) ``` We have a new element called environment. `epiviz-environment` enables brushing across all the charts in the current workspace and manages data. The environment also lets you set a genomic location to all its children charts. This will be more clear at the end of this vignette. First, Create an epiviz enivornment ```{r} epivizEnv <- epivizEnv(chr="chr11", start= 34000000, end = 39000000) ``` Lets add the hg19 reference genes track ```{r} genes_track <- epivizChart(Homo.sapiens, parent=epivizEnv) genes_track ``` Now, let's add the CpG island track included in this package. ```{r} data(cgi_gr) cgi_track <- epivizChart(cgi_gr, parent=epivizEnv, datasource_name="CpG Islands") cgi_track ``` Now, let's add a heatmap with the gene expression barcode data ```{r} data(bcode_eset) bcode_hmap <- epivizChart(bcode_eset, parent=epivizEnv, datasource_name="Gene Expression Barcode", chart="HeatmapPlot") bcode_hmap ``` Finally lets visualize all the charts in the environment. ```{r} epivizEnv ```