internals.R

## High level Helper functions

.import_biom <- function(input) {
  ## Select appropriate import_function
  import_function <- switch(input$biomFormat,
                            "std"   = import_biom,
                            "frogs" = import_frogs)
  ## Import
  return(import_function(input$fileBiom$datapath, ## biom file
                         input$fileTree$datapath  ## tree file
  ))
}

.import_sample_data <- function(input, physeq) {
  ## Unhappy path
  if (is.null(input$fileMeta)) {
    return(data.frame(SampleID = sample_names(physeq) , row.names = sample_names(physeq)))
  }

  ## Happy path: excel version
  if (input$CSVsep == "excel") {
    ## For efficiency and consistency, maybe replace with readr::read_xl
    sdf <- RcmdrMisc::readXL(input$fileMeta$datapath,
                             rownames = TRUE,
                             header = TRUE)
    sdf$SampleID <- rownames(sdf)
    return(sdf)
  }

  ## Happy path: csv version
  sdf <- read.csv(
    input$fileMeta$datapath,
    header = TRUE,
    sep = input$CSVsep,
    row.names = 1,
    na.strings = NA
  )
  sdf$SampleID <- rownames(sdf)
  return(sdf)
}

.format_tax_table <- function(tdf) {
  ## explicit rank names
  colnames(tdf) <- c("Kingdom", "Phylum", "Class", "Order",
                     "Family", "Genus", "Species", "Strain")[1:ncol(tdf)]
  ## Replace unknown by NA
  tdf[grep("unknown ", tdf)] <- NA
  #tdf[grep("Unclassified", tdf)] <- NA
  return(tdf)
}

.import_from_rdata <- function(input) {
  ## Happy path
  ne <- new.env() ## new env to store RData content and avoid border effects
  if (!is.null(input$fileRData))
    load(input$fileRData$datapath, envir = ne)
  if (class(ne$data) == "phyloseq")
    return(ne$data)

  ## Unhappy paths: everything else
  return()
}