Interactive construction of a ScanVcfParam object

ScanVcfParamShiny.R

scanVcfParamInteractive <- function(file) {

    asdf <- function(x) {
        df = data.frame(Field = rownames(x), Description = x$Description, Type = x$Type)
    }

    charIfNull <- function(x) {
        if(is.null(x)) {
            return(character())
        }
        x
    }
    
    x = scanVcfHeader(file)

    ui = pageWithSidebar(
        headerPanel("VCF header"),
        sidebarPanel(
            selectInput("info", "info", rownames(info(x)), multiple = TRUE),
            selectInput("fixed", "fixed", rownames(fixed(x)), multiple = TRUE),
            selectInput("geno", "geno", rownames(geno(x)), multiple = TRUE),
            selectInput("samples", "samples", samples(x), multiple = TRUE),
            actionButton("close_app", "Return")
        ),
        mainPanel(
            tabsetPanel(
                tabPanel("info_table", dataTableOutput("info_table")),
                tabPanel("fixed_table", dataTableOutput("fixed_table")),
                tabPanel("geno_table", dataTableOutput("geno_table"))
            )
        )
    )
    
    server = function(input, output) {
        observe({
            if(input$close_app == 0)
                return()
            res = ScanVcfParam(
                fixed = charIfNull(input$fixed),
                info = charIfNull(input$info),
                geno = charIfNull(input$geno),
                samples = charIfNull(input$samples))
            stopApp(res)
        })
        output$info_table = renderDataTable({
            asdf(info(x))
          })
        output$fixed_table = renderDataTable({
            asdf(fixed(x))
        })
        output$geno_table = renderDataTable({
            asdf(geno(x))
        })
    }
    runApp(list(ui = ui, server = server))
}


library(VariantAnnotation)
library(shiny)

fl = system.file("extdata", "chr22.vcf.gz", package = "VariantAnnotation")

res = scanVcfParamInteractive(fl) ## input: VCF file, output: ScanVcfParam object