HiCeekR: GUI for Hi-C data analysis

# 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)
# # }
#