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server.R
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### 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)
})