### 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



shinyServer(function(input, output,session) {

  #######################################################
  ##                                                   ##
  ##                    LOAD FILES                     ##
  ##                                                   ##
  #######################################################

  csvf <- callModule(csvFile, "datafile",stringsAsFactors = FALSE) #  Module for importing data


  ##########################################
  ######## Widget update and info         ##
  ##########################################

  source(file.path("server", "Utilities.R"), local = TRUE)$value # Utilities method (packages citations, fc step, zipdownload and panel redirection and project name)

  ##########################################
  ######## HOME page                      ##
  ##########################################

  source(file.path("server", "Datasummary.R"), local = TRUE)$value # Reactive function that return the indexes for the signficant genes
  source(file.path("server", "Rendertable.R"), local = TRUE)$value #  All the output csv except for the heatmap page that are in heatmapshiny source

  ##########################################
  ######## Volcano page                   ##
  ##########################################

  source(file.path("server", "Volcanoshiny.R"), local = TRUE)$value # Volcano plot

  ################################
  ######## PCA page             ##
  ################################

  source(file.path("server", "PCAshiny.R"), local = TRUE)$value # PCA plot function
  source(file.path("server", "PCAselgroup.R"), local = TRUE)$value # all parameters for pca plot and more

  ################################
  ######## Venn page            ##
  ################################

  source(file.path("server", "Venn.R"), local = TRUE)$value # Generate the vennlist and select the contrasts and send them to Jvenn
  source(file.path("server", "Venninter.R"), local = TRUE)$value # Selected intersection Venn mean and barplot from the data table with the export. TODO remove not valuable info
  source(file.path("server", "Trackervenn.R"), local = TRUE)$value # Tracker for Venn

  ################################
  ######## Venn GO              ##
  ################################

  source(file.path("server", "Vennquery.R"), local = TRUE)$value # Venn query DAVID

  ################################
  ######## Heatmap page         ##
  ################################
  
  source(file.path("server", "Checkboxhm.R"), local = TRUE)$value # Heatmap function for select specific groups
  source(file.path("server", "Changeheatmbut.R"), local = TRUE)$value # Change the heatmap button color
  source(file.path("server", "Hidevent.R"), local = TRUE)$value # Hide parameters such as number of clusters ... and tooltip for dist
  source(file.path("server", "Heatmapshiny.R"), local = TRUE)$value # Generate the heatmap
  source(file.path("server", "Trackerhm.R"), local = TRUE)$value # Tracker for heatmap parameters
  source(file.path("server", "GetDEgenes.R"), local = TRUE)$value # Subset dataframe restable (stat, comp and deg to list of dataframes)
  source(file.path("server", "Backgroundcolor.R"), local = TRUE)$value # Background color for the heatmap

  ##########################################
  ######## GO enrichissment               ##
  ##########################################

  source(file.path("server", "Shinygohm.R"), local = TRUE)$value # functional analysis by querying DAVID web service
  source(file.path("server", "Highchartshiny.R"), local = TRUE)$value # Convert output david table to json and send it to bubble.js

  ################################
  ######## cutheatmap page      ##
  ################################

  source(file.path("server", "Cutheatmap.R"), local = TRUE)$value # Generation of boxplot

  ##########################################
  ######## Contact chat                   ##
  ##########################################

  source(file.path("server", "Shinychat.R"), local = TRUE)$value # Chat for the app associated with the file Chat.rds
  source(file.path("server", "Groupstripshiny.R"), local = TRUE)$value # Utilities method (packages citations, fc step, zipdownload and panel redirection and project name)
  

})