Plot now reacts to selected LG and offspring, changing to selectize and...

Plot now reacts to selected LG and offspring, changing to selectize and adjusting number of plots accordingly might be interesting. out of bound error does pop up initially after estimation, maybe a system wait or something will resolve this issue

polyploid_vis/app.R

@@ -184,7 +184,7 @@ server <- function(input, output, session) {
   
   # update maplist selection
   observeEvent(input$i_link_map, {
-    file_list <- names(link_map())
+    file_list <- 1:length(link_map())
     updateSelectInput(session, 'choice_map', label = 'Linkage Groups', choices = file_list)
   })
   
@@ -204,7 +204,7 @@ server <- function(input, output, session) {
   output$table_phenotype <- DT::renderDataTable(phenotype())
   
   # table for linkage map file(s)
-  output$table_link_map <- DT::renderDataTable(link_map()[[rv$select_map()]])
+  output$table_link_map <- DT::renderDataTable(link_map()[[as.numeric(rv$select_map())]])
   
   # table for SNP dosage 
   output$table_dosage <- DT::renderDataTable(dosage())
@@ -234,7 +234,7 @@ server <- function(input, output, session) {
 
   # update LG selection IBD file
   observeEvent(input$go_estimate, {
-    updateSelectInput(session, 'choice_LG', label = 'Linkage Group', choices = names(IBD_est()))
+    updateSelectInput(session, 'choice_LG', label = 'Linkage Group', choices = 1:length(names(IBD_est())))
   })
   
   # retrieve LG selection
@@ -242,7 +242,7 @@ server <- function(input, output, session) {
 
   #update offspring selection
   observeEvent(input$choice_LG, {
-    updateSelectInput(session, 'choice_offspring', label = 'Offspring', choices = IBD_est()[[input$choice_LG]]$offspring)
+    updateSelectInput(session, 'choice_offspring', label = 'Offspring', choices = IBD_est()[[as.numeric(input$choice_LG)]]$offspring)
   })
   
   # retrieve offspring selection
@@ -251,9 +251,9 @@ server <- function(input, output, session) {
   # show haplotypes from estimated IBDs
   output$plot_haplo <- renderPlot(visualiseHaplo(IBD_list = IBD_est(),
                                                 display_by = "name",
-                                                linkage_group = 1,
-                                                select_offspring = IBD_est()[[1]]$offspring[3:11],
-                                                multiplot = c(3, 3))
+                                                linkage_group = as.numeric(rv$select_LG()),
+                                                select_offspring = rv$select_offspring(),
+                                                multiplot = c(1, 1))
   )
   
   output$plot_haplo_imp <- renderPlot(visualiseHaplo(IBD_list = IBD_imp(),