inst/audit-main/app.R

In ggiaever/gg_audit-master: Shiny Application to Help Audit Your Growth Curves

# 00 - setup --------------------------------------------------------------

## CRAN dependencies
library(shiny)
library(shinydashboard)
library(shinyalert)
library(ggplot2)
library(plater)

## remotes and local dependencies
library(readcg12)
library(readgp1)
library(readyg)
library(readbioscreen)
source(file.path("modules","input.R"))
source(file.path("modules","experiment-table.R"))
source(file.path("modules","quickview.R"))
source(file.path("modules","preprocess.R"))
source(file.path("modules","plate.R"))
source(file.path("modules","summarise.R"))
source(file.path("modules","explore.R"))
source(file.path("modules","output.R"))
library(mtpview1)
library(mtpview)
library(growr)

# 01 - UI -----------------------------------------------------------------

header <- dashboardHeader(title = 'AUDIT')

sidebar <- dashboardSidebar(
  sidebarMenu(
    menuItem("Input", tabName = "inp", icon = icon("upload")),
    menuItem("Preprocess", tabName = "pre", icon = icon("broom")),
    menuItem("PlotPlate", tabName = "pla", icon = icon("broom")),
    menuItem("Summarise", tabName = "sum", icon = icon("filter")),
    menuItem("Explore", tabName = "exp", icon = icon("eye"), badgeLabel = "experimental", badgeColor = "yellow"),
    menuItem("Output", tabName = "out", icon = icon("download"))
  )
)

body <- dashboardBody(
  tabItems(
    tabItem(tabName = "inp",
      fluidRow(
        box(autoFileInput("datafile"),
          title = tagList(span(icon("upload"), style = 'opacity:0.3;'), span("Input"))),
        experimentBoxUI('experiment')
      ),
      fluidRow(
        quickviewBoxUI('viewbox')
      )
    ),
    tabItem(tabName = "pre",
      fluidRow(
        preprocessTabContentsUI('preprocess'),
        tableOutput('preprocesstbl')
      )
    ),
    tabItem(tabName = "pla",
      fluidRow(
        plateUI('plate')

      )
    ),
    tabItem(tabName = "sum",
      summariseTabContentsUI("summarised")
    ),
    tabItem(tabName = "exp",
      exploreContentsUI("explore")
    ),
    tabItem(tabName = "out",
      fluidRow(
        box(
          title = tagList(span(icon("filter"), style = 'opacity:0.3;'), span("Summarise")),
          column(6,
            helpText("Tidied and preprocessed measures data"),
            downloadObjUI(id = "download1")
          ),
          column(6,
            helpText("Summarised data (one row per well per group)"),
            downloadObjUI(id = "download2")
          )
        )
      )
    )
  )
)

ui <- dashboardPage(header, sidebar, body)


# 02 - Server -------------------------------------------------------------

server <- function(input, output, session) {

  datafile <- callModule(autoFile, "datafile")
  experiment <- callModule(experimentBox, "experiment", datafile)
  viewbox <- callModule(quickviewBox, "viewbox", experiment, datafile)
  preprocess <- callModule(preprocessTabContents, 'preprocess', datafile)
  growth <- callModule(plateSERV, 'plate', preprocess)
  summarised <- callModule(summariseTabContents, 'summarised', preprocess)
  callModule(exploreContents, 'explore', summarised)
  callModule(downloadObj, id = "download1", data = preprocess, "measures-data")
  callModule(downloadObj, id = "download2", data = summarised, "summarised-data")

  output$preprocesstbl <- renderTable({
    head(preprocess())
  })


}

shinyApp(ui, server)