inst/doc/VisualizeSumExp.R

In epivizrChart: R interface to epiviz web components

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

## -----------------------------------------------------------------------------
data(sumexp)

## -----------------------------------------------------------------------------
epivizEnv <- epivizEnv(interactive = TRUE)
scatterplot <- epivizEnv$plot(sumexp, datasource_name="sumExp", columns=c("cancer", "normal"))

## -----------------------------------------------------------------------------
epivizNav <- epivizNav(chr="chr11", start=118000000, end=121000000, parent=epivizEnv, interactive = TRUE)

genes_track <- epivizNav$add_genome(Homo.sapiens, datasource_name="genes")
# region_scatterplot <- epivizNav$plot(sumexp, datasource_name="sumExp", columns=c( "cancer", "normal"))
region_linetrack <- epivizNav$plot(sumexp, datasource_name="sumExp", columns=c( "cancer", "normal"), chart="LineTrack")

## ---- eval=FALSE--------------------------------------------------------------
#  
#  app <- shinyApp(
#    ui=fluidPage(
#      uiOutput("epivizChart")
#    ),
#    server=function(input, output, session) {
#  
#      output$epivizChart <- renderUI({
#        epivizEnv$render_component(shiny=TRUE)
#      })
#  
#      epivizEnv$register_shiny_handler(session)
#    }
#  )
#  
#  app
#