HiCeekR: GUI for Hi-C data analysis

# runModule<-function(){
#     return(
#         output$moduleScreen<-shiny::renderUI({})
#
#         #leggi in reactive se lo stato è branch o reStart
#         #se branch crea nuovo progetto
#         #se reStart cancella fino ad un certo punto e riprendi la là
#         #agiorna lo stato nel reactive come "ready"
#
#         withProgress(message="please wait module pre processing", min=0, max=3, {
#             setProgress(message = 'Calculation in progress', detail = 'This may take a while...')
#             if (input$mainNav == 'Filtering' & file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
#
#                 #source ('DiffHiC_DetectInteraction.R')
#                 tool_DetectInteraction<-"Filmod"
#                 moduleUI_DetectInteraction<- "FilmodUI"
#                 moduleLoad_DetectInteraction<- "FilmodServer"
#                 setProgress(value = 1)
#                 output$filteringSlot <- shiny::renderUI ({
#                     get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='')
#                 })
#                 setProgress(value = 2)
#                 loadApp_DetectInteraction <- shiny::callModule(
#                     get(moduleLoad_DetectInteraction)
#                     , tool_DetectInteraction,
#                     stringsAsFactors = FALSE,
#                     wdPath = rea$anDir
#                 )
#                 setProgress(value = 3)
#             }
#         })
#
#         if (input$mainNav == 'Binning'
#             & file.exists(paste0(rea$anDir, 'info.tsv')) == TRUE ){
#
#             tool_Binning <- 'DiffHiC_BinningV2'
#
#             moduleUI_Binning <- paste0 (tool_Binning, '_UI')
#             moduleLoad_Binning <- paste0 (tool_Binning,'_Server')
#             output$binningSlot <-renderUI ({
#                 get(moduleUI_Binning) (tool_Binning,label='helpingUI')
#             })
#             loadApp_Binning <-callModule(get(moduleLoad_Binning), tool_Binning,
#                                          stringsAsFactors = FALSE,
#                                          wdPath = rea$anDir
#             )
#
#         }
#
#         if (input$mainNav == 'iterative' &
#             file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
#             tool_DiffHiC_Norm <- 'diffHic_Normalization'
#             moduleUI_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm, '_UI')
#             moduleLoad_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm,'_Server')
#             output$iterativeSlot<-renderUI ({
#                 get(moduleUI_DiffHiC_Norm) (tool_DiffHiC_Norm,label='iceUI')
#             })
#             loadApp_DiffHiC_Norm <- callModule(get(moduleLoad_DiffHiC_Norm),
#                                                tool_DiffHiC_Norm,
#                                                stringsAsFactors = FALSE,
#                                                wdPath = rea$anDir
#             )
#         }
#
#         if (input$mainNav == 'WavSis' &
#             file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
#             tool_chromoR <- 'chromoR_Normalization'
#             moduleUI_chromoR<- paste0 (tool_chromoR, '_UI')
#             moduleLoad_chromoR<- paste0 (tool_chromoR,'_Server')
#             output$WavSisSlot<- shiny::renderUI ({
#                 get(moduleUI_chromoR) (tool_chromoR,label='helpingUI')
#             })
#             loadApp_chromoR <-shiny::callModule(get(moduleLoad_chromoR),
#                                                 tool_chromoR,
#                                                 stringsAsFactors = FALSE,
#                                                 wdPath = rea$anDir
#             )
#         }
#
#         if (input$mainNav == 'TADsHMM' &
#             file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#
#             tool_hmm <- 'HMM_postProcessing'
#             moduleUI_hmm<- paste0 (tool_hmm, '_UI')
#             moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
#             output$hmmSlot<-renderUI ({
#                 get(moduleUI_hmm) (tool_hmm,label='helpingUI')
#             })
#             loadApp_hmm <-  callModule(get(moduleLoad_hmm), tool_hmm,
#                                        stringsAsFactors = FALSE,
#                                        wdPath=rea$anDir
#             )
#         }
#
#         if (input$mainNav == 'CompartmentsPCA' & file.exists(paste0(
#             rea$anDir, 'info.tsv'))==TRUE ){
#             #source ('pcaComp_postProcessing.R')
#             tool_pcaComp <- 'pcaComp_postProcessing'
#             moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
#             moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
#             output$pcaCompSlot<- shiny::renderUI({
#                 get(moduleUI_pcaComp) (tool_pcaComp,label='pcaUI')
#             })
#             loadApp_pcaComp <-  shiny::callModule(get(moduleLoad_pcaComp),
#                                                   tool_pcaComp,
#                                                   stringsAsFactors = FALSE,
#                                                   wdPath=rea$anDir)
#         }
#
#         if (input$mainNav == 'EpigeneticFeatures' &
#             file.exists(paste0(rea$anDir, 'info.tsv'))==TRUE ){
#             #source ('pca_postProcessing.R')
#             tool_pca <- 'pca_postProcessing'
#             moduleUI_pca<- paste0 (tool_pca, '_UI')
#             moduleLoad_pca<- paste0 (tool_pca,'_Server')
#             output$pcaSlot<-shiny::renderUI ({
#                 get(moduleUI_pca) (tool_pca,label='epifUI')
#             })
#             loadApp_pca <- shiny::callModule(get(moduleLoad_pca), tool_pca,
#                                              stringsAsFactors = FALSE,
#                                              wdPath=rea$anDir
#             )
#         }
#
#
#         # if (input$mainNav == 'Analysis' ){
#         #     source ('anSettings.R')
#         #     tool_anSettings <- 'anSettings'
#         #     moduleUI_anSettings<- paste0 (tool_anSettings, '_UI')
#         #     moduleLoad_anSettings<- paste0 (tool_anSettings,'_Server')
#         #     output$anSetPlot<-renderUI ({
#         #     get(moduleUI_anSettings) (tool_anSettings,label='helpingUI')
#         #     })
#         #     loadApp_anSettings <-  callModule(get(moduleLoad_anSettings), tool_anSettings,
#         #                                     stringsAsFactors = FALSE)
#         # }
#         #
#         # if (input$mainNav == 'Pre-Processing' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
#         #     source ('DiffHiC_DetectInteraction.R')
#         #     tool_DetectInteraction <- 'DiffHiC_DetectInteraction'
#         #     moduleUI_DetectInteraction<- paste0 (tool_DetectInteraction, '_UI')
#         #     moduleLoad_DetectInteraction<- paste0 (tool_DetectInteraction,'_Server')
#         #     output$preProSlot<-renderUI ({
#         #         get(moduleUI_DetectInteraction) (tool_DetectInteraction,label='helpingUI')
#         #     })
#         #     loadApp_DetectInteraction <-  callModule(get(moduleLoad_DetectInteraction), tool_DetectInteraction,
#         #                                             stringsAsFactors = FALSE)
#         #}
#         #
#         # if (input$mainNav == 'Binning' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
#         #     source ('DiffHiC_BinningV2.R')
#         #     tool_Binning <- 'DiffHiC_BinningV2'
#         #     moduleUI_Binning<- paste0 (tool_Binning, '_UI')
#         #     moduleLoad_Binning<- paste0 (tool_Binning,'_Server')
#         #     output$binningSlot<-renderUI ({
#         #         get(moduleUI_Binning) (tool_Binning,label='helpingUI')
#         #     })
#         #     loadApp_Binning <-callModule(get(moduleLoad_Binning), tool_Binning,
#         #                                     stringsAsFactors = FALSE)
#         # }
#         #
#         # if (input$mainNav == 'WavSis' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
#         #     source ('chromoR_Normalization.R')
#         #     tool_chromoR <- 'chromoR_Normalization'
#         #     moduleUI_chromoR<- paste0 (tool_chromoR, '_UI')
#         #     moduleLoad_chromoR<- paste0 (tool_chromoR,'_Server')
#         #     output$WavSisSlot<-renderUI ({
#         #     get(moduleUI_chromoR) (tool_chromoR,label='helpingUI')
#         #     })
#         #     loadApp_chromoR <-  callModule(get(moduleLoad_chromoR), tool_chromoR,
#         #                                     stringsAsFactors = FALSE)
#         # }
#         #
#         # if (input$mainNav == 'iterative' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
#         #     source ('diffHic_Normalization.R')
#         #     tool_DiffHiC_Norm <- 'diffHic_Normalization'
#         #     moduleUI_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm, '_UI')
#         #     moduleLoad_DiffHiC_Norm<- paste0 (tool_DiffHiC_Norm,'_Server')
#         #     output$iterativeSlot<-renderUI ({
#         #         get(moduleUI_DiffHiC_Norm) (tool_DiffHiC_Norm,label='helpingUI')
#         #   })
#         #     loadApp_DiffHiC_Norm <<-  callModule(get(moduleLoad_DiffHiC_Norm), tool_DiffHiC_Norm,
#         #                                         stringsAsFactors = FALSE)
#         # }
#         #
#         # if (input$mainNav == 'Epigenetic Features' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
#         #     source ('pca_postProcessing.R')
#         #     tool_pca <- 'pca_postProcessing'
#         #     moduleUI_pca<- paste0 (tool_pca, '_UI')
#         #     moduleLoad_pca<- paste0 (tool_pca,'_Server')
#         #     output$pcaSlot<-renderUI ({
#         #         get(moduleUI_pca) (tool_pca,label='helpingUI')
#         #     })
#         #     loadApp_pca <-  callModule(get(moduleLoad_pca), tool_pca,
#         #                             stringsAsFactors = FALSE)
#         # }
#         #
#         # if (input$mainNav == 'Compartments-PCA' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
#         #     source ('pcaComp_postProcessing.R')
#         #     tool_pcaComp <- 'pcaComp_postProcessing'
#         #     moduleUI_pcaComp<- paste0 (tool_pcaComp, '_UI')
#         #     moduleLoad_pcaComp<- paste0 (tool_pcaComp,'_Server')
#         #     output$pcaCompSlot<-renderUI ({
#         #     get(moduleUI_pcaComp) (tool_pcaComp,label='helpingUI')
#         #     })
#         #     loadApp_pcaComp <-  callModule(get(moduleLoad_pcaComp), tool_pcaComp,
#         #                                 stringsAsFactors = FALSE)
#         # }
#         #
#         #
#         # if (input$mainNav == 'TADs-HMM' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
#         #     source ('HMM_postProcessing.R')
#         #     tool_hmm <- 'HMM_postProcessing'
#         #     moduleUI_hmm<- paste0 (tool_hmm, '_UI')
#         #     moduleLoad_hmm<- paste0 (tool_hmm,'_Server')
#         #     output$hmmSlot<-renderUI ({
#         #         get(moduleUI_hmm) (tool_hmm,label='helpingUI')
#         #     })
#         #     loadApp_hmm <-  callModule(get(moduleLoad_hmm), tool_hmm,
#         #                                 stringsAsFactors = FALSE)
#         # }
#         #
#         #
#         # if (input$mainNav == 'Heatmap' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
#         #     source ('TADsV2_Visualization.R')
#         #     tool_tads <- 'TADsV2_Visualization'
#         #     moduleUI_tads<- paste0 (tool_tads, '_UI')
#         #     moduleLoad_tads<- paste0 (tool_tads,'_Server')
#         #     output$TADsModule<-renderUI ({
#         #     get(moduleUI_tads) (tool_tads,label='helpingUI')
#         #     })
#         #     loadApp_tads <-  callModule(get(moduleLoad_tads), tool_tads,
#         #                                 stringsAsFactors = FALSE)
#         # }
#         #
#         # if (input$mainNav == 'Networks' & file.exists(paste0(anFolder$hisave, 'info.tsv'))==TRUE ){
#         #     source ('networksV2_Visualization.R')
#         #     tool_net <- 'networksV2_Visualization'
#         #     moduleUI_net<- paste0 (tool_net, '_UI')
#         #     moduleLoad_net<- paste0 (tool_net,'_Server')
#         #     output$netModule<-renderUI ({
#         #     get(moduleUI_net) (tool_net,label='nets')
#         #     })
#         #     loadApp_net <-  callModule(get(moduleLoad_net), tool_net,
#         #                                 stringsAsFactors = FALSE)
#         # }
#
#
#     )
# }