## ----setup, eval=TRUE, include=FALSE---------------------------------------
library(epivizrChart)
library(shiny)
library(Homo.sapiens)
library(Rsamtools)
library(rtracklayer)

## --------------------------------------------------------------------------
data(cgi_gr)
data(bcode_eset)

## --------------------------------------------------------------------------
epivizNav <- epivizNav(chr="chr11", start=118000000, end=121000000, interactive=TRUE)
genes_track <- epivizNav$add_genome(Homo.sapiens)
blocks_track <- epivizNav$plot(cgi_gr, datasource_name="CpG_Islands")
means_track <- epivizNav$plot(bcode_eset, datasource_name="Gene Expression Barcode", chart="HeatmapPlot")

## --------------------------------------------------------------------------
file1 <- Rsamtools::BamFile("http://1000genomes.s3.amazonaws.com/phase3/data/HG01879/alignment/HG01879.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam")
file2 <- rtracklayer::BEDFile("https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz")

epiviz_igv <- epivizNav$plot(
                file1,
                datasource_name = "genes2")

## ---- eval=FALSE-----------------------------------------------------------
#  app <- shinyApp(
#    ui=fluidPage(
#      uiOutput("epivizChart")
#    ),
#    server=function(input, output, session) {
#  
#      output$epivizChart <- renderUI({
#        epivizNav$render_component(shiny=TRUE)
#      })
#  
#      # register for shiny events to manage data requests from UI
#      epivizNav$register_shiny_handler(session)
#    }
#  )
#  
#  app
#  

## ---- eval=FALSE-----------------------------------------------------------
#  app <- shinyApp(
#    ui=fluidPage(
#      textInput('gene_loc', 'Enter Genomic Location (example: chr11:119000000 - 120000000', "chr11:118000000-121000000"),
#      uiOutput("epivizChart")
#    ),
#    server=function(input, output, session) {
#  
#      renderEpiviz <- function() {
#        output$epivizChart <- renderUI({
#          epivizNav$render_component(shiny=TRUE)
#        })
#      }
#  
#      observeEvent(input$gene_loc, {
#        loc <- input$gene_loc
#        if(loc != "") {
#          chr_split <- strsplit(loc, ":")
#          chr <- chr_split[[1]][1]
#          range_split <- strsplit(chr_split[[1]][2], "-")
#  
#          epivizNav$navigate(chr = chr,
#                             start = strtoi(range_split[[1]][1]),
#                             end = strtoi(range_split[[1]][2]))
#        }
#        renderEpiviz()
#      })
#  
#      epivizNav$register_shiny_handler(session)
#    }
#  )
#  
#  app
#  

