Merge branch 'master' of forgemia.inra.fr:migale/affiliationexplorer

R/app_server.R

@@ -12,12 +12,14 @@ app_server <- function(input, output, session) {
   # List the first level callModules here
   
   shinyjs::hide("clean")
+  shinyjs::hide("skip")
   shinyjs::hide("download")
-  output$tmptxt <- renderUI("Please upload your data (Biom file and MultiHits TSV file).")
+  output$tmptxt <- renderUI(HTML("<p>Please upload your data (Biom file and MultiHits TSV file).</p>"))
   
   observeEvent(input$tsv, {
     
     shinyjs::show("clean")
+    shinyjs::show("skip")
     shinyjs::show("download")
     
     output$tmptxt <- renderUI("")
@@ -52,7 +54,7 @@ app_server <- function(input, output, session) {
       # Extract Affiliation for a given OTU
       data$affi <- extract_affiliation(affi, input$asv) %>% dplyr::distinct()
       amb <- find_level(data$affi)
-      output$txt <- renderUI({paste(input$asv, "- ", nrow(data$affi) ,"conflicting affiliation, ambiguity at rank ", amb)})
+      output$txt <- renderUI(HTML({paste("<p><b>", input$asv, "- ", nrow(data$affi) ,"conflicting affiliation, ambiguity at rank ", amb, "</b></p>")}))
       output$table <- DT::renderDT({data$affi}, 
                                    selection = list(mode = 'single', selected = NULL, target = 'row'), 
                                    editable = TRUE)
@@ -60,12 +62,12 @@ app_server <- function(input, output, session) {
       output$selection <- renderUI({
         s = input$table_rows_selected
         if (length(s)) {
-          paste(
-            "Current affiliation:",
-            paste(data$cleaned[input$asv, ], collapse = ';'), 
-            "to be replaced with:", 
-            paste(data$affi[s, ], collapse = ';'),
-            sep = "\n") 
+          
+          HTML(paste("<b>Current affiliation:</b><br/>&nbsp;&nbsp;&nbsp;"),
+               paste(data$cleaned[input$asv, ], collapse = ' / '),
+               "<br/><b>to be replaced with:</b><br/>&nbsp;&nbsp;&nbsp;",
+               paste(data$affi[s, ], collapse = ' / ')
+          )
         }
       })
     })
@@ -88,7 +90,21 @@ app_server <- function(input, output, session) {
                           selected = data$amb_otus[1]
         )
       }        
-    })
+    }
+    )
+    
+    ## Skip ASV
+    observeEvent(input$skip, {
+      
+      data$amb_otus <- setdiff(data$amb_otus, input$asv)
+      
+      updateSelectInput(session, "asv",
+                        label =  "Select ASV",
+                        choices = data$amb_otus,
+                        selected = data$amb_otus[1]
+      )
+    }
+    )
     
     output$download <- downloadHandler(
       filename = function() {

R/app_ui.R

@@ -37,10 +37,11 @@ app_ui <- function() {
                 htmlOutput("txt"),
                 HTML("<br/>"),
                 DT::DTOutput("table"),
-                HTML("<br/>"),
+                #HTML("<br/>"),
                 htmlOutput("selection"),
                 HTML("<br/>"),
                 actionButton("clean", "Clean ASV"),
+                actionButton("skip", "Skip ASV"),
                 downloadButton("download", "Download")
             )
           )