app.R

library(shiny)
library(VennDiagram)
library(stringr)
source("functions.R")

example_query<-scan_in("example_query")
example_reference<-scan_in("example_reference")
example_background<-scan_in("example_background")

u <- shinyUI(
    fluidPage(
        sidebarPanel(
            textAreaInput('vec1', 'Query values (newline delimited)'),
            textAreaInput('vec2', 'Reference values (newline delimited)'),
            textAreaInput('vec3', 'Background values (newline delimited)'),
            actionButton("run", "Run test"),
            actionButton("reset", "Reset"),
            actionButton("example", "Example")
        ),
        
        mainPanel(
            h3('Fisher test for enrichment'),
            br(),
            p("Test for enrichment of one list in another list, given a third, background list"),
            p("Enter newline delimited values in the relevant boxes to the left"),
            h3('Test result:'),
            verbatimTextOutput("show_results"),
            br(),
            imageOutput("venn_diagram")
        )
    ))

s <- shinyServer(function(input, output, session) {
    # print contigency table and results
    results<-eventReactive(input$run, {
        query <- unlist(strsplit(input$vec1,"\n"))
        ref <- unlist(strsplit(input$vec2,"\n"))
        back<- unlist(strsplit(input$vec3,"\n"))
        contingency<-contingency_table(query,ref,back)
        fisher<-fisher_test(contingency)
        results<-print_results(fisher)
        cat("Contingency table: \n\n")
        print(contingency)
        cat("\n")
        cat("Results: \n\n")
        cat(results)
    })
    
    # set up venn diagram
    venn<-eventReactive(input$run, {
        outfile <- tempfile(fileext='.png')
        png(outfile, width=400, height=300)
        draw_venn(input$vec1, input$vec2, input$vec3)
        dev.off()
        list(src = outfile,
             contentType = 'image/png',
             width = 400,
             height = 300,
             alt = "")
    })

    # shownresults and venn diagram on clicking run
    observeEvent(input$run, {
        output$show_results<-renderPrint({
            results()
        })
        output$venn_diagram <- renderImage({
            venn()
        })
    })
    
    # render empty text and plot blank on clicking reset
    observeEvent(input$reset, {
        output$show_results <- renderText({
        })
        updateTextInput(session, "vec1", value="")
        updateTextInput(session, "vec2", value="")
        updateTextInput(session, "vec3", value="")
        output$venn_diagram <- plot.new()
        dev.off()
            
    })
    
    # fill in inputs with example data on clicking example
    observeEvent(input$example, {
        output$show_results <- renderText({
        })
        updateTextInput(session, "vec1", value=example_query)
        updateTextInput(session, "vec2", value=example_reference)
        updateTextInput(session, "vec3", value=example_background)
    })
    
}
)

shinyApp(ui = u, server = s)