---
title: "Workshop: W5 - Shiny"
output:
  BiocStyle::html_document:
    toc: false
vignette: >
  % \VignetteIndexEntry{Workshop: W5 - Shiny}
  % \VignetteEngine{knitr::rmarkdown}
---

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
options(width=100, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))
```

```{r setup, echo=FALSE, messages=FALSE, warnings=FALSE}
suppressPackageStartupMessages({
    library(shiny)
    library(RNAseqData.HNRNPC.bam.chr14)
    library(Homo.sapiens)
    library(Gviz)
})
```

Author: Martin Morgan (<a
  href="mailto:mtmorgan@fredhutch.org">mtmorgan@fredhutch.org</a>)<br/ >
Date: 7 September, 2015<br />
Back to [Workshop Outline](Developer-Meeting-Workshop.html)<br />

The material in this document requires _R_ version 3.2 and
_Bioconductor_ version 3.1

```{r configure-test}
stopifnot(
    getRversion() >= '3.2' && getRversion() < '3.3',
    BiocInstaller::biocVersion() >= "3.1"
)
```

# Interactive visualization -- `shiny`

Writing a [shiny](http://shiny.rstudio.com) app

- 'User interface' describing what the user sees
- 'Server' implementing the logic that transforms user selections to
  outputs
- Very interesting 'reactive' programming model; sort of like an Excel
  spread sheet, where changing a cell causes a formula in another cell
  to update.

A simple directory with user interface (`ui.R`) and server
(`server.R`) _R_ scripts

- User interface, file `ui.R`

    ```{r shiny-ui, eval=FALSE}
    library(shiny)
    library(RNAseqData.HNRNPC.bam.chr14)
    library(Homo.sapiens)
    
    ## Get all SYMBOLs on chr14
    symbols <- keys(Homo.sapiens, keytype="SYMBOL")
    map <- select(Homo.sapiens, symbols, "TXCHROM", "SYMBOL")
    symchoices <- sort(unique(map$SYMBOL[map$TXCHROM %in% "chr14"]))
    
    ## Possible BAM files
    bamchoices <- basename(RNAseqData.HNRNPC.bam.chr14_BAMFILES)
    
    ## Define the user interface
    shinyUI(fluidPage(
    
        ## Application title
        titlePanel("BAMSpector: Reads Supporting Gene Models"),
    
        sidebarLayout(
            sidebarPanel(
                ## input gene symbol (fancy: select from available)
                selectInput("symbol", "Gene Symbol", symchoices),
    
                ## input path to BAM file
                selectInput("bam", "BAM File", bamchoices, multiple=TRUE)),
    
            ## Show a plot of the generated distribution
            mainPanel(plotOutput("tracksPlot")))
        ))
    ```

- Server, file `server.R`

    ```{r shiny-server, eval=FALSE}
    ## load required libraries
    library(shiny)
    library(RNAseqData.HNRNPC.bam.chr14)
    library(Homo.sapiens)
    library(Gviz)
    
    ## where are the BAM files?
    dirname <- unique(dirname(RNAseqData.HNRNPC.bam.chr14_BAMFILES))
    
    ## What are the ranges of each gene?
    ranges <- genes(Homo.sapiens, columns="SYMBOL")
    ranges$SYMBOL <- unlist(ranges$SYMBOL)
    
    ## Create a representation of each gene region
    genes <- GeneRegionTrack(TxDb.Hsapiens.UCSC.hg19.knownGene,
                             chromosome="chr14")
    
    shinyServer(function(input, output) {
    
        output$tracksPlot <- renderPlot({
            if (length(input$bam) > 0) {
                ## coverage on each BAM file
                bam <- file.path(dirname, input$bam)
                coverage <- Map(DataTrack,
                    range = bam, name = bam,
                    MoreArgs=list(type = 'histogram',
                        window = -1, genome = 'hg19',
                        chromosome = 'chr14'))
            } else {
                coverage <- list()
            }
    
            ## Select the correct range
            range <- ranges[match(input$symbol, ranges$SYMBOL)]
    
            ## plot the GeneRegionTrack and coverage
            plotTracks(c(list(genes), coverage),
                       from = start(range), to=end(range),
                       chr='chr14', windowSize = 30)
        })
    })
    ```

- Application

    ```{r shiny-launch, eval=FALSE}
    shiny::runApp()
    ```