inst/shiny/benchmarks.R

In toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

output$downloadBenchmarks <- downloadHandler(

  filename = "Benchmarks.csv",

  content = function(filename) {
    write.csv(get_benchmarks(), filename, row.names = FALSE)
  }
)

get_benchmarks <- reactive({

  groupCol <- epDF[["groupColName"]]
  assays <- epDF[["assays"]]
  flags <- epDF[["flags"]]
  sites <- epDF[["sites"]]
  groups <- epDF[["group"]]
  removeFlags <- all_flags[!(all_flags %in% flags)]
  rawData <- rawData()

  if(!is.null(rawData)) {
    if(all(is.null(rawData$benchmarks))) {

      ACC <- get_ACC(rawData$chem_info$CAS)
      ACC <- remove_flags(ACC, flag_id = removeFlags)

      remove_groups <- unique(cleaned_ep[[groupCol]])[which(!unique(cleaned_ep[[groupCol]]) %in% groups)]
      remove_groups <- remove_groups[!is.na(remove_groups)]

      filtered_ep <- filter_groups(cleaned_ep,
                                   groupCol = groupCol,
                                   remove_assays = assays,
                                   remove_groups = remove_groups)

      bench <- ACC %>%
        dplyr::filter(endPoint %in% filtered_ep$endPoint) %>%
        dplyr::rename(Value = ACC_value,
               Chemical = chnm) %>%
        dplyr::left_join(filtered_ep, by = "endPoint") |> 
        dplyr::group_by(dplyr::across(c(-flags))) |> 
        dplyr::summarise(flags = paste0(unlist(flags), collapse = "|")) |>
        dplyr::ungroup()

    } else {
      bench <- rawData$benchmarks
    }
  }

  return(bench)
})