server.R

library(shinydashboard)

shinyServer
(function(input, output, session)
{
  checkNull <- function(x) {
    if (!exists(as.character(substitute(x)))) {
      return(NULL)
    } else if (is.null(x)) {
      return(NULL)
    } else if (length(x) > 1) {
      return(x)
    }
    else if (x %in% c(0, "", NA, "NULL")) {
      return(NULL)
    } else {
      return(x)
    }
  }
  
  beautifulTable <- function(data)  {
    DT::datatable(
      data = data,
      rownames = FALSE,
      filter = "top",
      extensions = c("Buttons", "ColReorder", "FixedColumns"),
      options = list(
        dom = "lBtip",
        pageLength = 10,
        lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
        buttons = list(
          'colvis',
          list(
            extend = 'collection',
            buttons = c('copy', 'csv', 'excel', 'pdf'),
            text = 'Download'
          )
        ),
        colReorder = TRUE,
        scrollX = TRUE,
        fixedColumns = list(leftColumns = 1, rightColumns = 0)
      ),
      width = "auto",
      height = "auto"
    )
  }
  
  source(
    "https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/R/load-extra-functions.R"
  )
  
  data16S <- reactive({
    if (input$biomFormat == "std")
    {
      d <- import_biom(
        BIOMfilename = input$fileBiom$datapath,
        treefilename = input$fileTree$datapath,
        refseqfilename = input$fileSeq$datapath
      )
    } else if (input$biomFormat == "frogs") {
      d <- import_frogs(
        biom = input$fileBiom$datapath,
        treefilename = input$fileTree$datapath,
        refseqfilename = input$fileSeq$datapath
      )
    }
    
    colnames(tax_table(d)) <-
      c("Kingdom",
        "Phylum",