Upload 18 files

app/js/index.js

@@ -1,3 +1,25 @@
 export function maximizeBox() {
   
+}
+
+
+export function create_legend(titles, colors) {
+	  let legend_div = document.getElementById('legend');
+	
+    let legend_item = document.createElement('div');
+    let col_circle = document.createElement('div');
+    let legend_span = document.createElement('span');
+
+    legend_item.classList.add('legend-item');
+    col_circle.classList.add('legend-col-circle');
+    legend_span.classList.add('legend-span');
+
+    col_circle.style.backgroundColor = color;
+    legend_span.textContent = title;
+
+    legend_item.append(col_circle);
+    legend_item.append(legend_span);
+
+    legend_div.append(legend_item);
+
 }

app/logic/create_sankey.R

@@ -2,7 +2,7 @@
 box::use(
   data.table[...],
   stats[na.omit],
-  plotly[plot_ly, layout],
+  plotly[plot_ly, layout, add_annotations],
 )
 
 #' sankey_preprare_data
@@ -37,14 +37,15 @@ box::use(
 sankey_prepare_data <- function(dataset, selected_pathways, selected_genes, is_pathway) {
   # filter the selected_pathways -> | gene_name | kegg_paths_name |
   if (!is_pathway) {
-    sankey_data <- dataset[gene_name %in% selected_genes$gene_name, .(gene_name, kegg_paths_name, var_name)]
+    sankey_data <- dataset[gene_name %in% selected_genes$gene_name, .(gene_name, kegg_paths_name, var_name, col)]
   } else {
-    sankey_data <- dataset[kegg_paths_name %in% selected_pathways$pathway, .(gene_name, kegg_paths_name, var_name)]
+    sankey_data <- dataset[kegg_paths_name %in% selected_pathways$pathway, .(gene_name, kegg_paths_name, var_name, col)]
   }
 
   setorder(sankey_data, kegg_paths_name, gene_name)
   labels_all <- data.table(
     label = c(sankey_data$kegg_paths_name, sankey_data$gene_name, sankey_data$var_name)
+
   )
   # get all labels their id
   labels_all[, id := match(labels_all$label, unique(labels_all$label))]
@@ -57,6 +58,7 @@ sankey_prepare_data <- function(dataset, selected_pathways, selected_genes, is_p
   full <- unique(na.omit(with_source))
   path_gene <- unique(full[, .(kegg_paths_name, gene_name, first, second)])
   scores <- c(rle(rleid(c(full$first + full$second)))$lengths, rep(1, nrow(full)))
+  scores <- rep(1, length(scores))
   return(list(labels, full, scores))
 }
 
@@ -71,17 +73,21 @@ sankey_prepare_data <- function(dataset, selected_pathways, selected_genes, is_p
 #' @export
 #'
 #' @examples
-create_sankey <- function(labels, path_gene, gene_variant, scores) {
+create_sankey <- function(labels, path_gene, gene_variant, scores, colors) {
+  path_gene_labels <- labels
+  path_gene_labels[(nrow(labels) - length(unique(gene_variant$var_name)) + 1):nrow(labels)]$label <- ""
+  
   fig <- plot_ly(
     type = "sankey",
     orientation = "h",
     selectedpoints = c(0:10),
     node = list(
-      label = labels$label,
-      #x = c(rep(0, length(unique(path_gene$kegg_paths_name))), rep(1, length(unique(gene_variant$gene_name))), rep(2, length(unique(gene_variant$var_name)))),
+      label = path_gene_labels$label,
       y = seq(0, nrow(labels), by = 1),
       color = "black",
       pad = 30,
+      customdata = labels$label,
+      hovertemplate = paste("%{customdata}"),
       thickness = 30,
       line = list(
         color = "black",
@@ -91,13 +97,30 @@ create_sankey <- function(labels, path_gene, gene_variant, scores) {
     link = list(
       source = c(path_gene$first, gene_variant$second) - 1,
       target = c(path_gene$second, gene_variant$third) - 1,
-      value = scores
+      value = scores,
+      color = colors
     )
   )
+
+
+  
+  fig <- fig |> add_annotations(x = 0, y = -0.1, showarrow = FALSE, font = list(size = 17), xref = "x", yref = "paper", text = "Pathway")
+  fig <- fig |> add_annotations(x = 1, y = -0.1, showarrow = FALSE, font = list(size = 17), xref = "x", yref = "paper", text = "Gene")
+  fig <- fig |> add_annotations(x = 2, y = -0.1, showarrow = FALSE, font = list(size = 17), xref = "x", yref = "paper", text = "Variant")
   
   fig <- fig |> layout(
     font = list(
       size = 14
+    ),
+    xaxis = list(
+      showgrid = FALSE,
+      zeroline = FALSE,
+      visible = FALSE
+    ),
+    yaxis = list(
+      showgrid = FALSE,
+      zeroline = FALSE,
+      visible = FALSE
     )
   )
   fig

app/logic/data_preprocessor.R

@@ -1,7 +1,8 @@
 
 box::use(
   data.table[...],
-  stats[na.omit]
+  stats[na.omit],
+  RColorBrewer[brewer.pal]
 )
 
 
@@ -61,11 +62,17 @@ preprocess_maf_data <- function() {
            new = c("ensembl_id", "gene_name", "Allele")
   )
   
+
   variants_tab <- na.omit(variants_tab)
-  genes_sample <- sample(variants_tab$gene_name, 2000)
+  genes_sample <- variants_tab$gene_name
+  
   variants_tab <- variants_tab[gene_name %in% genes_sample]
   variants_tab[, var_name := paste0(Chromosome, "_", Start_Position, "_", Reference_Allele, "/", Allele)]
   tab <- variants_tab[kegg_tab, on = "ensembl_id", nomatch = 0, allow.cartesian = TRUE]
+  
+  variant_types <-unique(tab$Variant_Type)
+  colors_tab <- data.table(col = brewer.pal(length(variant_types), "Set2"), Variant_Type = variant_types)
+  tab <- tab[colors_tab, on = "Variant_Type"]
   return(tab)
   
 }

app/main.R

@@ -1,13 +1,14 @@
 box::use(
-  shiny[bootstrapPage, div, icon, moduleServer, fluidRow, NS, renderUI, tags, uiOutput],
+  shiny[...],
   bs4Dash[box, dashboardPage, tabItems, tabItem, sidebarMenu, menuItem, dashboardHeader, column, dashboardBrand, dashboardSidebar, dashboardBody],
   thematic[thematic_shiny],
   shinyjs[useShinyjs, runjs],
-  gargoyle[init]
+  gargoyle[init],
+  utils[globalVariables]
 )
+globalVariables(c("mutation.table.df", "hgnc2pfam.df"))
 
 library(g3viz)
-
 box::use(
   app/logic/data_preprocessor[preprocess_data],
   app/logic/data_preprocessor[preprocess_maf_data]
@@ -17,7 +18,8 @@ box::use(
   app/view/table,
   app/view/sankey,
   app/view/lollipop,
-  app/view/browser
+  app/view/browser,
+  app/view/plot_options
 )
 
 thematic_shiny()
@@ -72,6 +74,7 @@ ui <- function(id) {
           fluidRow(
             column(
               width = 9,
+              plot_options$ui(ns("plot_options")),
               sankey$ui(ns("sankey")),
               lollipop$ui(ns("lollipop"))
             ),
@@ -99,17 +102,32 @@ ui <- function(id) {
   )
 }
 
+
+whole_dataset <- preprocess_maf_data()
+
 #' @export
 server <- function(id) {
   moduleServer(id, function(input, output, session) {
     init("reset_sankey")
-    shiny::devmode()
-    
+
+    ns <- NS(id)
+    data <- reactiveVal(whole_dataset)
+    options <- plot_options$server("plot_options", unique(data()$Variant_Type), unique(data()$Consequence))
+    observeEvent(options(), {
+      req((length(options()[[1]]) > 0 || length(options()[[2]] > 0)))
+
+      selected_var_types <- options()[[1]]
+      selected_consequences <- options()[[2]]
+      
+      tab <- whole_dataset[Variant_Type %in% selected_var_types]
+      data(tab[Consequence %in% selected_consequences])
+      
+    })
+
     # data <- preprocess_data()
-    data <- preprocess_maf_data()
-    print(data)
-    browser$server("browser", data)
-    selected_features <- table$server("table", data)
+    browser$server("browser", data())
+    
+    selected_features <- table$server("table", data())
     selected_gene_rval <- sankey$server("sankey", data, selected_features()[[1]], selected_features()[[2]], selected_features()[[3]])
     lollipop$server("lollipop", data, selected_gene_rval)
   })

app/static/css/app.min.css

@@ -1 +1 @@
-.toggle-switch{position:relative;display:inline-block;width:40px;height:24px;margin:10px}.toggle-switch .toggle-input{display:none}.toggle-switch .toggle-label{position:absolute;top:0;left:0;width:40px;height:24px;background-color:#ccc;border-radius:34px;cursor:pointer;transition:background-color .3s}.toggle-switch .toggle-label::before{content:"";position:absolute;width:20px;height:20px;border-radius:50%;top:2px;left:2px;background-color:#fff;box-shadow:0px 2px 5px 0px rgba(0,0,0,.3);transition:transform .3s}.toggle-switch .toggle-input:checked+.toggle-label{background-color:#2196f3}.toggle-switch .toggle-input:checked+.toggle-label::before{transform:translateX(16px)}.toggle-switch.light .toggle-label{background-color:#bebebe}.toggle-switch.light .toggle-input:checked+.toggle-label{background-color:#9b9b9b}.toggle-switch.light .toggle-input:checked+.toggle-label::before{transform:translateX(6px)}.toggle-switch.dark .toggle-label{background-color:#4b4b4b}.toggle-switch.dark .toggle-input:checked+.toggle-label{background-color:#717171}.toggle-switch.dark .toggle-input:checked+.toggle-label::before{transform:translateX(16px)}.feat-radio-container{display:flex;justify-content:center;align-items:center}.feat-radio-container>h4{margin-top:6px}.toggle-switch-feat{position:relative;display:inline-block;width:40px;height:24px;margin:10px}.toggle-switch-feat .toggle-input-feat{display:none}.toggle-switch-feat .toggle-label-feat{position:absolute;top:0;left:0;width:40px;height:24px;background-color:#bbb;border-radius:34px;cursor:pointer;transition:background-color .3s}.toggle-switch-feat .toggle-label-feat::before{content:"";position:absolute;width:20px;height:20px;border-radius:50%;top:2px;left:2px;background-color:#fff;box-shadow:0px 2px 5px 0px rgba(0,0,0,.3);transition:transform .3s}.toggle-switch-feat .toggle-input-feat:checked+.toggle-label-feat{background-color:#bbb}.toggle-switch-feat .toggle-input-feat:checked+.toggle-label-feat::before{transform:translateX(16px)}.toggle-switch-feat.light .toggle-label-feat{background-color:#bebebe}.toggle-switch-feat.light .toggle-input-feat:checked+.toggle-label-feat{background-color:#9b9b9b}.toggle-switch-feat.light .toggle-input-feat:checked+.toggle-label-feat::before{transform:translateX(6px)}.toggle-switch-feat.dark .toggle-label-feat{background-color:#4b4b4b}.toggle-switch-feat.dark .toggle-input:checked+.toggle-label-feat{background-color:#717171}.toggle-switch-feat.dark .toggle-input-feat:checked+.toggle-label-feat::before{transform:translateX(16px)}.header-btns{width:100%;display:flex;justify-content:space-between}.shiny-output-error-validation{color:#000046;font-size:22px}
+.toggle-switch{position:relative;display:inline-block;width:40px;height:24px;margin:10px}.toggle-switch .toggle-input{display:none}.toggle-switch .toggle-label{position:absolute;top:0;left:0;width:40px;height:24px;background-color:#ccc;border-radius:34px;cursor:pointer;transition:background-color .3s}.toggle-switch .toggle-label::before{content:"";position:absolute;width:20px;height:20px;border-radius:50%;top:2px;left:2px;background-color:#fff;box-shadow:0px 2px 5px 0px rgba(0,0,0,.3);transition:transform .3s}.toggle-switch .toggle-input:checked+.toggle-label{background-color:#2196f3}.toggle-switch .toggle-input:checked+.toggle-label::before{transform:translateX(16px)}.toggle-switch.light .toggle-label{background-color:#bebebe}.toggle-switch.light .toggle-input:checked+.toggle-label{background-color:#9b9b9b}.toggle-switch.light .toggle-input:checked+.toggle-label::before{transform:translateX(6px)}.toggle-switch.dark .toggle-label{background-color:#4b4b4b}.toggle-switch.dark .toggle-input:checked+.toggle-label{background-color:#717171}.toggle-switch.dark .toggle-input:checked+.toggle-label::before{transform:translateX(16px)}.feat-radio-container{display:flex;justify-content:center;align-items:center}.feat-radio-container>h4{margin-top:6px}.toggle-switch-feat{position:relative;display:inline-block;width:40px;height:24px;margin:10px}.toggle-switch-feat .toggle-input-feat{display:none}.toggle-switch-feat .toggle-label-feat{position:absolute;top:0;left:0;width:40px;height:24px;background-color:#bbb;border-radius:34px;cursor:pointer;transition:background-color .3s}.toggle-switch-feat .toggle-label-feat::before{content:"";position:absolute;width:20px;height:20px;border-radius:50%;top:2px;left:2px;background-color:#fff;box-shadow:0px 2px 5px 0px rgba(0,0,0,.3);transition:transform .3s}.toggle-switch-feat .toggle-input-feat:checked+.toggle-label-feat{background-color:#bbb}.toggle-switch-feat .toggle-input-feat:checked+.toggle-label-feat::before{transform:translateX(16px)}.toggle-switch-feat.light .toggle-label-feat{background-color:#bebebe}.toggle-switch-feat.light .toggle-input-feat:checked+.toggle-label-feat{background-color:#9b9b9b}.toggle-switch-feat.light .toggle-input-feat:checked+.toggle-label-feat::before{transform:translateX(6px)}.toggle-switch-feat.dark .toggle-label-feat{background-color:#4b4b4b}.toggle-switch-feat.dark .toggle-input:checked+.toggle-label-feat{background-color:#717171}.toggle-switch-feat.dark .toggle-input-feat:checked+.toggle-label-feat::before{transform:translateX(16px)}.header-btns{width:100%;display:flex;justify-content:space-between}.shiny-output-error-validation{color:#000046;font-size:22px}.flex-centered{display:flex;align-items:center;justify-content:center}.awesome-checkbox{margin-left:15px !important;margin-right:15px !important}.flex-col{flex-direction:column}.control-label{font-size:18px}#legend{height:30px;display:flex;flex-direction:row;justify-content:center;align-items:center}.legend-span{padding:10px}.legend-item{display:flex;justify-content:center;align-items:center}.legend-col-circle{width:15px;height:15px;border-radius:50%}

app/styles/misc.scss

@@ -14,4 +14,53 @@ $light-red: #dc3545;
 .shiny-output-error-validation {
   color: $dark-blue;
   font-size: 22px;
-}
+}
+
+
+.flex-centered {
+  display: flex;
+  align-items: center;
+  justify-content: center;
+}
+
+.awesome-checkbox {
+  margin-left: 15px !important;
+  margin-right: 15px !important ;
+}
+
+.flex-col {
+  flex-direction: column;
+}
+
+
+.control-label {
+  font-size: 18px;
+}
+
+
+
+
+#legend {
+    height: 30px;
+    display: flex;
+    flex-direction: row;
+    justify-content: center;
+    align-items: center;
+  }
+  
+  .legend-span {
+    padding: 10px;
+  }
+  
+  .legend-item {
+    display: flex;
+    justify-content: center;
+    align-items: center;
+  }
+  
+  
+  .legend-col-circle {
+    width: 15px;
+    height: 15px;
+    border-radius: 50%;
+  }

app/view/lollipop.R

@@ -27,8 +27,7 @@ server <- function(id, data, selected_gene_rval) {
 
     output$lollipop_plot <- renderG3Lollipop({
       req(selected_gene_rval())
-      print(selected_gene_rval())
-      filter_tab <- data[gene_name == selected_gene_rval()]
+      filter_tab <- data()[gene_name == selected_gene_rval()]
       plot.options <- g3Lollipop.theme(theme.name = "cbioportal",
                                        title.text = selected_gene_rval(),
                                        y.axis.label = "# of Mutations")

app/view/plot_options.R

@@ -0,0 +1,59 @@
+box::use(
+  shiny[moduleServer, NS, div, observeEvent, req, reactive, textOutput, renderText, uiOutput, renderUI],
+  shinyWidgets[awesomeCheckboxGroup, pickerInput, pickerOptions],
+  bs4Dash[box]
+
+)
+
+#' @export
+ui <- function(id) {
+  ns <- NS(id)
+  box(
+    width = 12,
+    title = "Plot options",
+    status = "navy",
+    maximizable = TRUE,
+    solidHeader = TRUE,
+    div(
+      class = "flex-centered, flex-col",
+      uiOutput(ns("filter_var_type_UI")),
+      uiOutput(ns("filter_consequence_UI"))
+    )
+  )
+}
+
+#' @export
+server <- function(id, var_types, conseq_types) {
+  moduleServer(id, function(input, output, session) {
+    
+    ns <- session$ns # so that we put the renderui inputs in the same namespace as the session
+    
+    output$filter_var_type_UI <- renderUI({
+      awesomeCheckboxGroup(
+        inputId = ns("pick_var_type"),
+        label = "Filter variant type",
+        choices = var_types,
+        selected = var_types,
+        inline = TRUE
+      )
+    })
+    
+    output$filter_consequence_UI <- renderUI({
+      labels <- gsub(",", ", ", gsub("_", " ", conseq_types))
+      names(conseq_types) <- labels
+      pickerInput(
+        inputId = ns("pick_consequence"),
+        label = "Select consequence types", 
+        choices = conseq_types,
+        selected = conseq_types,
+        multiple = TRUE,
+        options = pickerOptions(container = "body", 
+                                actionsBox = TRUE),
+        width = "100%"
+      )
+    })
+    
+    
+    return(reactive(list(input$pick_var_type, input$pick_consequence)))
+  })
+}

app/view/sankey.R

@@ -1,8 +1,10 @@
 box::use(
-  shiny[moduleServer, verbatimTextOutput, renderPrint, isolate, NS, req, validate, need, tagList, renderPlot, plotOutput, observeEvent, reactiveVal, reactiveValues],
+  shiny[moduleServer, observe, reactive, br, div, verbatimTextOutput, renderPrint, isolate, NS, req, validate, need, tagList, renderPlot, plotOutput, observeEvent, reactiveVal, reactiveValues],
   plotly[plot_ly, event_data, plotlyOutput, renderPlotly, plotlyProxy, plotlyProxyInvoke],
   data.table[...],
+  purrr[map2],
   bs4Dash[box],
+  graphics[legend, mtext],
   stats[na.omit],
   shinyjs[...],
   gargoyle[...]
@@ -16,17 +18,17 @@ box::use(
 ui <- function(id) {
   ns <- NS(id)
   tagList(
-    
     box(
       width = 12,
-      height = "50vh",
+      height = "54vh",
       title = "Sankey Diagram",
       status = "navy",
       maximizable = TRUE,
       solidHeader = TRUE,
       id = ns("sankey_box"),
+      div(id = "legend"),
       plotlyOutput(ns("sankey_plt"), height = "50vh")
-      
+      #plotOutput(ns("sankey_legend"))
     )
   )
 }
@@ -36,7 +38,6 @@ server <- function(id, dataset, selected_pathways_react, selected_genes_react, i
   moduleServer(id, function(input, output, session) {
     ns <- NS(id)
     # reactive value holding the sankey plot
-    
 
 # reactiveVal initialization ----------------------------------------------
 
@@ -52,11 +53,17 @@ server <- function(id, dataset, selected_pathways_react, selected_genes_react, i
 # Render ------------------------------------------------------------------
 
     output$sankey_plt <- renderPlotly({
+      
       validate(
         need(!((is.null(selected_pathways_react()) || nrow(selected_pathways_react()) == 0)
                && (is.null(selected_genes_react()) || nrow(selected_genes_react()) == 0)),
              "select the features (pathways / genes) that you want to visualize from the table on the right")
       )
+      
+      legend_tab <- unique(dataset()[, .(Variant_Type, col)])
+      prepare_legend_r()
+      map2(.x = legend_tab$Variant_Type, .y = legend_tab$col, \(title, color) add_to_legend_r(title, color))
+
       # output the contents of the sankey_plot reactive value
       if (is_path_tab_active()) {
         sankey_pathway_plot()
@@ -66,6 +73,7 @@ server <- function(id, dataset, selected_pathways_react, selected_genes_react, i
     })
     
     
+    
 
 # Events ------------------------------------------------------------------
 
@@ -79,36 +87,41 @@ server <- function(id, dataset, selected_pathways_react, selected_genes_react, i
     }) 
     
     # data is passed into module -> create sankey
-    observeEvent(selected_pathways_react(), {
-      req(selected_pathways_react())
-
-      data <- sankey_prepare_data(dataset, selected_pathways_react(), selected_genes_react(), TRUE)
+    observe({
+      
+      if (is_path_tab_active()) {
+        req(selected_pathways_react())
+      }
+      else {
+        req(selected_genes_react())
+      }
+      
+      data <- sankey_prepare_data(dataset(), selected_pathways_react(), selected_genes_react(), is_path_tab_active())
       labels(data[[1]])
       path_gene <- unique(data[[2]][, .(kegg_paths_name, gene_name, first, second)])
-      gene_variant <- unique(data[[2]][, .(gene_name, var_name, second, third)])
+      gene_variant <- unique(data[[2]][, .(gene_name, var_name, col, second, third)])
       setorder(path_gene, first)
       setorder(gene_variant, second)
       path_gene_tab(path_gene)
       gene_variant_tab(gene_variant)
       
-      plot <- create_sankey(labels(), path_gene, gene_variant, data[[3]])
-      sankey_pathway_plot(plot)
+      
+      colors <- NULL
+      if (nrow(labels()) > 0) {
+        colors <- c(rep("lightgray", nrow(path_gene)), gene_variant$col) 
+
+      }
+      plot <- create_sankey(labels(), path_gene, gene_variant, data[[3]], colors)
+      
+      if (is_path_tab_active()) {
+        sankey_pathway_plot(plot)
+      }
+      else {
+        sankey_gene_plot(plot)
+      }
     })
     
-    observeEvent(selected_genes_react(), {
-      req(selected_genes_react())
-      print(selected_genes_react())
-      data <- sankey_prepare_data(dataset, selected_pathways_react(), selected_genes_react(), FALSE)
-      labels(data[[1]])
-      path_gene <- unique(data[[2]][, .(kegg_paths_name, gene_name, first, second)])
-      gene_variant <- unique(data[[2]][, .(gene_name, var_name, second, third)])
-      setorder(path_gene, first)
-      setorder(gene_variant, second)
-      path_gene_tab(path_gene)
-      gene_variant_tab(gene_variant)
-      plot <- create_sankey(labels(), path_gene, gene_variant, data[[3]])
-      sankey_gene_plot(plot)
-    })
+
     
     
     observeEvent(event_data("plotly_click", priority = "event"), {
@@ -122,7 +135,7 @@ server <- function(id, dataset, selected_pathways_react, selected_genes_react, i
     
       link_colors <- rep("lightgray", nrow(labels()))
       link_colors[link_ids] <- "red"
-
+      
       proxy <- plotlyProxy("sankey_plt", session)
       plotlyProxyInvoke(proxy, "restyle",
                         list(link.color = list(link_colors)))
@@ -130,6 +143,9 @@ server <- function(id, dataset, selected_pathways_react, selected_genes_react, i
     })
     
     
+    
+    
+    
     observeEvent(input$sankey_box$maximized, {
       plot_height <- if (input$sankey_box$maximized) {
         "100%"
@@ -224,4 +240,39 @@ second_level_link_selection <- function(clicked_link, path_gene_tab, gene_varian
   return(list(link_ids, select_gene_name))
 }
 
+prepare_legend_r <- function() {
+  js_call <- "
+    let legend_div = document.getElementById('legend');
+    legend_div.textContent = '';
+  "
+  shinyjs::runjs(js_call)
+}
+
+add_to_legend_r <- function(title, color) {
+  js_call <- sprintf(
+    "
+
+	  let legend_div = document.getElementById('legend');
+	
+    let legend_item = document.createElement('div');
+    let col_circle = document.createElement('div');
+    let legend_span = document.createElement('span');
+
+    legend_item.classList.add('legend-item');
+    col_circle.classList.add('legend-col-circle');
+    legend_span.classList.add('legend-span');
 
+    legend_span.textContent = '%s';
+    col_circle.style.backgroundColor = '%s';
+
+    legend_item.append(col_circle);
+    legend_item.append(legend_span);
+
+    legend_div.append(legend_item);
+    
+    
+    console.log('DONE');
+    "
+  , title, color)
+  shinyjs::runjs(js_call)
+}

app/view/table.R

@@ -27,12 +27,12 @@ ui <- function(id) {
         HTML(
           '
                   <div id="feat-radio" style="margin-left: 15px" class="feat-radio-container">
-                    <h4>Pathway</h4>
+                    <h4>Gene</h4>
                     <div class="toggle-switch-feat">
                       <input  name="checkbox-feature" class="toggle-input-feat" id="toggle-feat" type="checkbox">
                       <label class="toggle-label-feat" for="toggle-feat"></label>
                     </div>
-                    <h4>Gene</h4>
+                    <h4>Pathway</h4>
                   </div>
 
                   <script>
@@ -40,9 +40,9 @@ ui <- function(id) {
                   var checkbox = document.querySelector("input[name=checkbox-feature]");
                   checkbox.addEventListener("change", function() {
                     if (this.checked) {
-                      Shiny.setInputValue("app-table-feature_radio", "gene", {priority: "event"});
-                    } else {
                       Shiny.setInputValue("app-table-feature_radio", "pathway", {priority: "event"});
+                    } else {
+                      Shiny.setInputValue("app-table-feature_radio", "gene", {priority: "event"});
                     }
                   });
 
@@ -64,7 +64,7 @@ ui <- function(id) {
 server <- function(id, data) {
   
   moduleServer(id, function(input, output, session) {
-    is_path_tab_active <- reactiveVal(TRUE)
+    is_path_tab_active <- reactiveVal(FALSE)
     selected_pathways <- reactiveVal(NULL)
     selected_genes <- reactiveVal(NULL)
     
@@ -78,11 +78,11 @@ server <- function(id, data) {
       unique(data[, .(gene_name)])
     })
     
-    observeEvent(pathways_tab(),{
-      req(pathways_tab())
-      output$table <- render_pathways_table(
-        pathways_tab(),
-        selected_pathways()
+    observeEvent(genes_tab(),{
+      req(genes_tab())
+      output$table <- render_genes_table(
+        genes_tab(),
+        selected_genes()
       )
     })
 
@@ -137,7 +137,6 @@ server <- function(id, data) {
       row <- input$table_cell_clicked[["row"]]
       req(gene)
       if (is.null(row)) {
-        print("it is null")
         return(NULL)
       }
       
@@ -151,7 +150,6 @@ server <- function(id, data) {
         features[, row_i := rows]
         selected_genes(features)
       }
-      print(selected_pathways())
     })
     
     return(reactiveVal(list(selected_pathways, selected_genes, is_path_tab_active)))