### Author: Franck Soubès
### Bioinformatics Master Degree - University of Bordeaux, France
### Link: https://github.com/GeT-TRiX/MA_Trix_App/
### Where: GET-TRiX's facility
### Application: MATRiX is a shiny application for Mining and functional Analysis of TRanscriptomics data
### Licence: GPL-3.0


#######################################################
######## grep gene family                             #
#######################################################


#' genetodisplay is a reactive function that return an uppercase character vector
#'
#' @param fillvolc A reactive character input with genes separated by comma
#'
#' @return An uppercase character vector
#'
#' @export


genetodisplay <- reactive({
  if(is.null(input$fillvolc))
    return(NULL)
  else{
    if(!input$fillvolc == "")
      mycol = gsub("^\\s+|\\s+$", "", unlist(strsplit(input$fillvolc, ",")))
    else
      mycol = ""
    return(toupper(mycol))
  }
})


#' family_input is a reactive function that return a reactive character
#'
#' @param findfamily A reactive character input
#'
#' @return A reactive character
#'
#' @export


family_input <- reactive({
  input$findfamily
})


family_d <- shiny::debounce(family_input, 1200) # Delay input debounche also pour search genes

top_volc <- reactive({
  ifelse(input$topvolc==0, NA, input$topvolc)
})


top_volcd <- shiny::debounce(top_volc, 1000) # Delay input debounche also pour search genes



#######################################################
######## parse gene symbol for min and maj            #
#######################################################

#' familytopdisp is a reactive function that return a character vector of genes with uppercase
#'
#' @param family_d A reactive character with debounce attribute
#' @param csvf A reactive data frame
#'
#' @return An uppercase reactive character vector
#'
#' @export


familytopdisp <- reactive({
  if(is.null(family_d))
    return(NULL)
  else{
    if(!family_d() == ""){
      genfam = grep(pattern = toupper(family_d()), toupper(csvf()[[3]]$GeneName)) %>% slice(csvf()[[3]],.)%>% select(GeneName)  %>% unlist() %>% as.character()
    }
    else
      genfam =""
    return(toupper(genfam))
  }
})


#######################################################
######## Desactivate volcano input dep on user choice #
#######################################################


observe({ #hide or show inputs
	shinyjs::toggleState("topvolc", input$findfamily == "" & input$fillvolc == "")
	shinyjs::toggleState("findfamily", input$topvolc == 0 & input$fillvolc == "")
	shinyjs::toggleState("fillvolc", input$topvolc == 0 & input$findfamily == "")



})


#################################################
######## Plot and save volcano                  #
#################################################

#' volcano is a reactive function that return ggplotobject
#'
#'
#' @return A reactive ggplot object
#'
#' @export


volcano <- reactive({
  req(csvf(),input$volcacomp )
  EnhancedVolcano(csvf()[[3]], lab= csvf()[[3]]$GeneName , x = paste0(prefstat$greppre[[2]],input$volcacomp) ,
                  y = paste0(ifelse(input$method == "FDR",prefstat$greppre[[1]] ,prefstat$greppre[[3]]),input$volcacomp),
                  topgenes = ifelse(top_volcd() == 0, NA,top_volcd()),DrawConnectors= T,#DrawConnectors = ifelse(is.na(input$topvolc),T,F),
                  pCutoff = input$volcpval ,FCcutoff = input$volcfc ,transcriptPointSize = input$volcpt,transcriptLabSize = input$volclab,
                  title =  gsub("-"," versus " ,input$volcacomp),colAlpha=input$volcalpha, cutoffLineType = "twodash", findfamily =  ifelse(familytopdisp() == "" , NA,familytopdisp()),regulationvolc = input$regulationvolc,
                  displaylab = ifelse(genetodisplay() =="", NA, genetodisplay()),legendLabSize = 10,
                  cutoffLineCol = "black",cutoffLineWidth = 1,legend=c("NS","Log (base 2) fold-change","P value",
                                                                       "P value & Log (base 2) fold-change"))
})

volcboth <- reactiveValues()
volcobj <- reactiveValues()


output$volcanoplot <- renderPlot({

  validate(need(csvf(), 'You need to import data to visualize this plot!'))

  req(volcano())
  volcboth$tot <- volcano()
  volcobj$plot <- volcboth$tot[[1]]
  volcobj$dt <-volcboth$tot[[2]]
  volcobj$plot

},  height = plotHeight)

output$compvolc <- renderUI({
  req(subsetstat())
  selectInput("volcacomp", "Choose a comparison", choices = colnames(subsetstat()[[1]]))
})


callModule(downoutputfiles, "savevolc", projectname = projectname , suffix= "_volcano." , data = reactive(volcano()[[1]]),  w = 12, h = 12 ,volcform = T)

#' vocfilt is a reactive function that return a reactive dataframe
#'
#' @param volcobj A reactivevalue dataframe of the displayed genes
#' @param volcacomp A reactive character input
#' @param regulationvolc A reactive character input
#' @param volcanocomp A reactive character vector
#' @param prefstat A reactivevalue character (prefix FC)
#' 
#' @return a reactive dataframe with computed mean for duplicated genes
#'
#' @export


vocfilt <- reactive({
  req(csvf(), top_volcd(),  volcanocomp())
  volcobj$top <- meanrankgenes(volcobj$dt, prefstat$greppre[[2]] , input$volcacomp,  volcanocomp(), input$regulationvolc  )
  return(volcobj$top)
})




volcanocomp <- reactive({
  return(c(input$volcacomp, input$addvolcacomp))
})

#' volcplototp is a reactive function that return a reactive ggplot object of the top n displayed genes
#'
#'
#' @return A reactive ggplot object
#'
#' @export


volcplototp <- reactive({
  req(vocfilt())

  selcomp <-  paste0(prefstat$greppre[[2]],  volcanocomp())
  myplot <- topngenes(vocfilt(), selcomp ,top_volcd()  ,meandup = "genes")
  return(myplot)
})




observe({

output$barplotvolc <- renderPlot({
  validate(need(top_volcd(), 'Add an input in the max number of genes widget!'))
    req(volcplototp())
    plotOutput(volcplototp())
  })

})

callModule(downoutputfiles, "savebarvolc", projectname = projectname , suffix= "_volc_barplot." , data = volcplototp, w=16 , h=7  )




output$addcompvolc <- renderUI({
  req(input$volcacomp)
  compleft <- names(subsetstat()[[1]])[!names(subsetstat()[[1]]) %in% input$volcacomp]
  selectizeInput(
  'addvolcacomp', 'Add comparison(s) for the barplot', choices = compleft, multiple = TRUE
  )
})