Changed IBD page to include more options for estimate_IBD function. importing...

Changed IBD page to include more options for estimate_IBD function. importing .rds file possible but not yet function, needs a switch of some sort

polyploid_vis/app.R

@@ -10,6 +10,7 @@ library(readr)
 library(shiny)
 library(shinybusy)
 library(polyqtlR)
+library(parallel)
 
 # UI ----
 # Define page layout, fluidPage automatically adjusts to user border dimensions
@@ -57,33 +58,60 @@ ui <-  fluidPage(
                       )
              ),
              
-             navbarMenu(# IBD page ----
-               'IBD', # change to IBD with import + compute
-               tabPanel('Heuristic',
+             tabPanel(# IBD page ----
+                      'IBD',
                         sidebarLayout(
                           sidebarPanel(
-                            h3('Estimation settings'),
+                            h3('Estimation'),
+                            
+                            # method of estimation
+                            selectInput(inputId = 'IBD_method',
+                                        label = 'Estimation Method',
+                                        choices = c('Heuristic'= 'heur', 
+                                                    'HMM' = 'hmm')),
+                            
+                            # mapping function
+                            selectInput(inputId = 'IBD_map',
+                                        label = 'Mapping Function',
+                                        choices = c('Haldane' = 'haldane',
+                                                    'Kosambi' = 'kosambi')),
+                            
                             
                             # Ploidy level indicator
                             numericInput(inputId = 'ploidy', 
                                          label = 'Ploidy level',
-                                         value = 4),
+                                         min = 2,
+                                         value = 4,
+                                         step = 2),
+                            
+                            # cores selection
+                            numericInput(inputId = 'IBD_core',
+                                        label = 'Numbers of processing cores',
+                                        min = 1,
+                                        value = 1,
+                                        max = detectCores() - 2),
                             
                             # Estimate starter
                             actionButton('heu_estimate',
-                                         label = 'Estimate IBD')
+                                         label = 'Estimate IBD'),
+                            
+                            hr(),
+                            
+                            h3('Import'),
+                            
+                            # IBD input
+                            fileInput(inputId = 'i_IBD',
+                                      label = 'Phenotype file')
                             ),
+                          
                             
                           mainPanel(
-                            h3('Output heuristic method'),
+                            h3('Output'),
                             
                             plotOutput('plot_haplo')
                           )
                         )
                       ),
-               tabPanel('HMM'),
-               tabPanel('Import')
-            ),
              
              
              tabPanel('QTL visualisation'),
@@ -168,26 +196,21 @@ server <- function(input, output, session) {
   # table for linkage map file(s)
   output$table_link_map <- DT::renderDataTable(link_map()[[rv$linkage_select()]])
   
-  # test text
-  output$text_link_map <- eventReactive(input$map_choice,
-                                        {rvname <- rv$linkage_select()
-                                        print(rvname)
-                                        print(link_map()[[rvname]])
-                                          })
-  
   # table for SNP dosage 
   output$table_dosage <- DT::renderDataTable(dosage())
   
   # table for IBD probability 
   output$table_IBD <- DT::renderDataTable(IBD())
   
-  # IBD imputation ----
-  # Heuristic IBD estimation
-  heu_IBD <- eventReactive(input$heu_estimate, {
+  # IBD estimationputation ----
+  # IBD estimation
+  IBD <- eventReactive(input$heu_estimate, {
     estimate_IBD(phased_maplist = link_map(),
                  genotypes = as.matrix(dosage()),
+                 method = input$IBD_method,
+                 map_function = input$IBD_map,
                  ploidy = input$ploidy,
-                 ncores = 2)
+                 ncores = input$IBD_core)
   })
   
   # Modal window to prevent interaction
@@ -197,7 +220,7 @@ server <- function(input, output, session) {
   })
   
   # show table heuristic IBDs
-  output$plot_haplo <- renderPlot(visualiseHaplo(IBD_list = heu_IBD(),
+  output$plot_haplo <- renderPlot(visualiseHaplo(IBD_list = IBD(),
                                                 display_by = "name",
                                                 linkage_group = 1,
                                                 select_offspring = colnames(dosage())[3:11],