upload app directory

app/js/index.js

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+export function maximizeBox() {
+  
+}

app/logic/__init__.R

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+# Logic: application code independent from Shiny.
+# https://go.appsilon.com/rhino-project-structure

app/logic/create_sankey.R

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+
+box::use(
+  data.table[...],
+  stats[na.omit],
+  plotly[plot_ly, layout],
+)
+
+#' sankey_preprare_data
+#' @description
+#' The purpose of this function is to wrangle the data to such a form that
+#' it plotly sankey can be made from it. 
+#' 
+#'
+#' @param dataset A data table coming from preprocess_data function, it has the
+#' following columns:
+#'  Consequence | given_ref | Allele | var_name | ensembl_id | biotype |
+#'  gene_name | variant_class | chrom | pos | all_kegg_gene_names | refseq_id |
+#'  kegg_paths_id | kegg_paths_name
+#' @param selected_pathways a data.table of selected pathways for filtering.
+#'  The table has having the following structure:
+#'        
+#'    | pathway | row_i |
+#     1: Endocytosis     5
+#'
+#' @return list of two data.tables and one vector:
+#' - labels is a table with two columns:
+#' | label | id |
+#' COVID-19 | 1 |
+#' 
+#' - full has the following columns:
+#' gene_name | kegg_paths_name | var_name | first | second | third
+#' 
+#' - scores is a vector of values
+#' @export
+#'
+#' @examples
+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$gene_name, .(gene_name, kegg_paths_name, var_name)]
+  } else {
+    sankey_data <- dataset[kegg_paths_name %in% selected_pathways$pathway, .(gene_name, kegg_paths_name, var_name)]
+  }
+
+  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$label))]
+  labels <- unique(labels_all)
+  
+  with_source <- sankey_data[labels, on = c(kegg_paths_name = "label")]
+  with_source <- with_source[labels, on = c(gene_name = "label")]
+  with_source <- with_source[labels, on = c(var_name = "label")]
+  setnames(with_source, old = c("id", "i.id", "i.id.1"), new = c("first", "second", "third"))
+  full <- unique(na.omit(with_source))
+  path_gene <- unique(full[, .(kegg_paths_name, gene_name, first, second)])
+  scores <- c(rle(rleid(c(full$first + full$second)))$lengths, rep(1, nrow(full)))
+  return(list(labels, full, scores))
+}
+
+
+
+#' Title
+#'
+#' @param labels 
+#' @param sankey_data 
+#'
+#' @return
+#' @export
+#'
+#' @examples
+create_sankey <- function(labels, path_gene, gene_variant, scores) {
+  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)))),
+      y = seq(0, nrow(labels), by = 1),
+      color = "black",
+      pad = 30,
+      thickness = 30,
+      line = list(
+        color = "black",
+        width = 2
+      )
+    ),
+    link = list(
+      source = c(path_gene$first, gene_variant$second) - 1,
+      target = c(path_gene$second, gene_variant$third) - 1,
+      value = scores
+    )
+  )
+  
+  fig <- fig |> layout(
+    font = list(
+      size = 14
+    )
+  )
+  fig
+}

app/logic/data_preprocessor.R

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+
+box::use(
+  data.table[...],
+  stats[na.omit]
+)
+
+
+#' preprocess_data
+#' @description
+#' This function loads the datasets tsvs, merges them and filters the columns
+#' 
+#'
+#' @return table with the following columns:
+#' Consequence | given_ref | Allele | var_name | ensembl_id | biotype |
+#' gene_name | variant_class | chrom | pos | all_kegg_gene_names | refseq_id |
+#' kegg_paths_id | kegg_paths_name
+#' @export
+#'
+#' @examples
+preprocess_data <- function() {
+  data_dir <- file.path("data/")
+  
+  variants_tab_full <- fread(file.path(data_dir, "all_variants.annotated.processed.tsv"), na.strings = c(".", "-"))
+  kegg_tab <- fread(file.path(data_dir, "kegg_tab.tsv"))
+  
+  variants_tab <- variants_tab_full[, .(Consequence, GIVEN_REF, Allele, Protein_position, HGVSp, Amino_acids, var_name, Gene, BIOTYPE, SOURCE, SYMBOL, VARIANT_CLASS, chrom, pos)]
+  variants_tab <- variants_tab[!is.na(variants_tab$HGVSp)]
+  variants_tab <- variants_tab[SOURCE == "Ensembl"]
+  
+  setnames(variants_tab,
+           old = c("Gene", "GIVEN_REF", "BIOTYPE", "SYMBOL", "VARIANT_CLASS", "Consequence", "Protein_position", "Amino_acids"),
+           new = c("ensembl_id", "given_ref", "biotype", "gene_name", "variant_class", "consequence", "protein_pos", "amino_acids"))
+  
+  ## join the tables
+  tab <- variants_tab[kegg_tab, on = "ensembl_id", nomatch = 0]
+  tab[, `:=`(gene_definition = NULL, SOURCE = NULL, type = NULL)]
+  return(tab)
+}
+
+
+
+
+#' preprocess_maf_data
+#' @description
+#' This function loads the datasets tsvs, merges them and filters the columns
+#' 
+#'
+#' @return table 
+#' @export
+#'
+#' @examples
+preprocess_maf_data <- function() {
+  data_dir <- file.path("data/")
+  kegg_tab <- fread(file.path(data_dir, "kegg_tab.tsv"))[, .(ensembl_id, kegg_paths_name)]
+  kegg_tab <- kegg_tab[ensembl_id != ""]
+  mutations_data <- fread(file.path(data_dir, "brca_tcga_pub2015/data_mutations.txt"), sep = "\t")
+  
+  variants_tab <- mutations_data[, .(Hugo_Symbol, Gene, Chromosome, Start_Position, End_Position, Strand, Consequence, Variant_Classification, Variant_Type, Reference_Allele, Tumor_Seq_Allele2, HGVSc, HGVSp, Protein_position, Codons)]
+  setnames(variants_tab,
+           old = c("Gene", "Hugo_Symbol", "Tumor_Seq_Allele2"),
+           new = c("ensembl_id", "gene_name", "Allele")
+  )
+  
+  variants_tab <- na.omit(variants_tab)
+  genes_sample <- sample(variants_tab$gene_name, 2000)
+  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]
+  return(tab)
+  
+}

app/logic/render_table.R

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+
+
+#' render_genes_table
+#'
+#' @param all_pathways_tab a data table with a single column e.g.
+#'  | gene_name |
+#'    RPL22
+#' @param selected a (1-based) vector of indices of selected genes
+#' - used if we have been using pathways table and now we have switched back to
+#'  genes tab and want to rerender the table, keeping the genes that we selected
+#'  previously
+#'
+#' @return rendered DT table 
+#' @export
+#'
+#' @examples
+render_genes_table <- function(gene_tab, selected = NULL) {
+  print(selected)
+  DT::renderDT({
+   
+    DT::datatable(
+      gene_tab,
+      escape = FALSE,
+      selection = list(
+        mode = "multiple",
+        selected = selected,
+        target = "row"
+      ),
+      options = list(
+        pageLength = 15
+      )
+    )
+  })
+}
+
+
+#' render_pathways_table
+#'
+#' @param all_pathways_tab a data table with a single column e.g.
+#'  | pathway |
+#'    Covid-19
+#' @param selected a (1-based) vector of indices of selected pathways
+#' - used if we have been using gene table and now we have switched back
+#'  to pathways and want to rerender the table, keeping the pathways that
+#'  we selected previously
+#'
+#' @return rendered DT table 
+#' @export
+#'
+#' @examples
+render_pathways_table <- function(all_pathways_tab, selected = NULL) {
+  print(selected)
+  DT::renderDT({
+    tab <- DT::datatable(
+      all_pathways_tab,
+      escape = FALSE,
+      selection = list(
+        mode = "multiple",
+        selected = selected,
+        target = "row"
+      ),
+      callback = htmlwidgets::JS('
+                                  table.on("mouseover", "td", function() {
+                                  var index = table.cell(this).index();
+                                  Shiny.setInputValue("table-hover_pathway_genes", index, {priority: "event"});
+                                   })'),
+      options = list(pageLength = 15)
+    )
+
+    return(tab)
+  })
+}

app/main.R

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+box::use(
+  shiny[bootstrapPage, div, icon, moduleServer, fluidRow, NS, renderUI, tags, uiOutput],
+  bs4Dash[box, dashboardPage, tabItems, tabItem, sidebarMenu, menuItem, dashboardHeader, column, dashboardBrand, dashboardSidebar, dashboardBody],
+  thematic[thematic_shiny],
+  shinyjs[useShinyjs, runjs],
+  gargoyle[init]
+)
+
+box::use(
+  app/logic/data_preprocessor[preprocess_data],
+  app/logic/data_preprocessor[preprocess_maf_data]
+)
+
+box::use(
+  app/view/table,
+  app/view/sankey,
+  app/view/lollipop,
+  app/view/browser
+)
+
+thematic_shiny()
+
+#' @export
+ui <- function(id) {
+  ns <- NS(id)
+  dashboardPage(
+    header = dashboardHeader(
+      title = "VarWiz",
+      skin = "dark",
+      status = "white"
+    ),
+    dark = NULL,
+    help = NULL,
+    sidebar = dashboardSidebar(
+      collapsed = TRUE,
+      status = "navy",
+      skin = "dark",
+      sidebarMenu(
+        id = "side_menu",
+        div(class = "menu-tab", menuItem("Visualization", tabName = "visualization_tab", icon = icon("chart-line"))),
+        div(class = "menu-tab", menuItem("Browse data", tabName = "browse_tab", icon = icon("table"))),
+        div(class = "menu-tab", menuItem("About", tabName = "about_tab", icon = icon("book-open"))),
+        div(class = "menu-tab", menuItem("Start Tutorial", tabName = "tutorial", icon = icon("play")))
+      )
+    ),
+    body = dashboardBody(
+      tags$head(
+        tags$script(
+          "$(function() {
+              $('[data-card-widget=\"maximize\"]').on('click', function() {
+                setTimeout(function() {
+                  var isMaximized = $('html').hasClass('maximized-card');
+                  if (isMaximized) {
+                    $('#app-sankey-sankey').css('height', '1000px');
+                  } else {
+                    $('#app-sankey-sankey').css('height', '400px');
+                  }
+                }, 300);
+                $('#app-sankey-sankey').trigger('resize');
+              });
+            });
+            "
+        )
+      ),
+      
+      useShinyjs(),
+      tabItems(
+        tabItem(
+          tabName = "visualization_tab",
+          fluidRow(
+            column(
+              width = 9,
+              sankey$ui(ns("sankey")),
+              lollipop$ui(ns("lollipop"))
+            ),
+            column(
+              width = 3,
+              table$ui(ns("table")),
+            ),
+          )
+        ),
+        
+        tabItem(
+          tabName = "browse_tab",
+          browser$ui(ns("browser"))
+          
+        ),
+        
+        tabItem(
+          tabName = "about_tab"
+        )
+      )
+      
+      
+      
+    )
+  )
+}
+
+#' @export
+server <- function(id) {
+  moduleServer(id, function(input, output, session) {
+    init("reset_sankey")
+    
+    # data <- preprocess_data()
+    data <- preprocess_maf_data()
+    browser$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

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+.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}

app/styles/main.scss

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+@import 'toggle_switches';
+@import 'misc';

app/styles/misc.scss

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+$dark-blue: #000046;
+$light-blue: #1CB5E0;
+$full-red: #cc1425;
+$light-red: #dc3545;
+
+.header-btns {
+    width: 100%;
+    display: flex;
+    justify-content: space-between;
+
+}
+
+
+.shiny-output-error-validation {
+  color: $dark-blue;
+  font-size: 22px;
+}

app/styles/toggle_switches.scss

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+.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 0.3s;
+}
+
+.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, 0.3);
+  transition: transform 0.3s;
+}
+
+.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);
+}
+
+/* CHECKBOX FEATURE */
+
+.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 0.3s;
+}
+
+.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, 0.3);
+  transition: transform 0.3s;
+}
+
+.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);
+}

app/view/__init__.R

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+# View: Shiny modules and related code.
+# https://go.appsilon.com/rhino-project-structure

app/view/browser.R

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+box::use(
+  shiny[moduleServer, NS, h1, fluidRow, column],
+  DT[renderDT, dataTableOutput],
+  htmlwidgets[JS]
+)
+
+#' @export
+ui <- function(id) {
+  ns <- NS(id)
+  fluidRow(
+    column(
+      width = 12,
+      dataTableOutput(ns("browser_table"))
+    )
+  )
+
+}
+
+#' @export
+server <- function(id, dataset) {
+  moduleServer(id, function(input, output, session) {
+    output$browser_table <- renderDT({
+      
+
+      DT::datatable(
+        dataset,
+        options = list(
+          scrollX = TRUE,
+          scrollCollapse = TRUE,
+          initComplete = JS(
+            "function(settings, json) {",
+            "$(this.api().table().header()).css({'background-color': '#001f3f', 'color': 'white'});",
+            "}")
+        )
+      )
+    })
+  })
+}

app/view/lollipop.R

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+box::use(
+  shiny[...],
+  bs4Dash[box],
+  g3viz[...]
+)
+
+#' @export
+ui <- function(id) {
+  ns <- NS(id)
+  tagList(
+    
+    box(
+      width = 12,
+      status = "navy",
+      solidHeader = TRUE,
+      align = "center",
+      title = "Lollipop plot",
+      id = "lollipop_plot_box",
+      g3LollipopOutput(ns("lollipop_plot"), height = "700px")
+    )
+  )
+}
+
+#' @export
+server <- function(id, data, selected_gene_rval) {
+  moduleServer(id, function(input, output, session) {
+
+    output$lollipop_plot <- renderG3Lollipop({
+      req(selected_gene_rval())
+      print(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")
+
+      g3viz::g3Lollipop(
+        mutation.dat = filter_tab,
+        gene.symbol = selected_gene_rval(),
+        gene.symbol.col = "gene_name",
+        aa.pos.col = "Protein_position",
+        protein.change.col = "HGVSp",
+        factor.col = "Consequence",
+        btn.style = "gray", # gray-style chart download buttons
+        plot.options = plot.options,
+      )
+    })
+  })
+}

app/view/sankey.R

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+box::use(
+  shiny[moduleServer, verbatimTextOutput, renderPrint, isolate, NS, req, validate, need, tagList, renderPlot, plotOutput, observeEvent, reactiveVal, reactiveValues],
+  plotly[plot_ly, event_data, plotlyOutput, renderPlotly, plotlyProxy, plotlyProxyInvoke],
+  data.table[...],
+  bs4Dash[box],
+  stats[na.omit],
+  shinyjs[...],
+  gargoyle[on]
+)
+
+box::use(
+  app/logic/create_sankey[sankey_prepare_data, create_sankey]
+)
+
+#' @export
+ui <- function(id) {
+  ns <- NS(id)
+  tagList(
+    
+    box(
+      width = 12,
+      height = "50vh",
+      title = "Sankey Diagram",
+      status = "navy",
+      maximizable = TRUE,
+      solidHeader = TRUE,
+      id = ns("sankey_box"),
+      plotlyOutput(ns("sankey_plt"), height = "50vh")
+      
+    )
+  )
+}
+
+#' @export
+server <- function(id, dataset, selected_pathways_react, selected_genes_react, is_path_tab_active) {
+  moduleServer(id, function(input, output, session) {
+    ns <- NS(id)
+    # reactive value holding the sankey plot
+    
+
+# reactiveVal initialization ----------------------------------------------
+
+    sankey_plot <- reactiveVal()
+    sankey_pathway_plot <- reactiveVal()
+    sankey_gene_plot <- reactiveVal()
+    labels <- reactiveVal()
+    path_gene_tab <- reactiveVal()
+    gene_variant_tab <- reactiveVal()
+    selected_gene_name <- reactiveVal()
+    
+
+# 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")
+      )
+      # output the contents of the sankey_plot reactive value
+      if (is_path_tab_active()) {
+        sankey_pathway_plot()
+      } else {
+        sankey_gene_plot()
+      }
+    })
+    
+    
+
+# Events ------------------------------------------------------------------
+
+    
+    on("reset_sankey", {
+      if (is_path_tab_active()) {
+        sankey_pathway_plot(NULL)
+      } else {
+        sankey_gene_plot(NULL)
+      }
+    }) 
+    
+    # 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)
+      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_pathway_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"), {
+      click_data <- event_data("plotly_click", priority = "event")
+      req(click_data)
+      
+      result <- sankey_link_selection(click_data, path_gene_tab(), gene_variant_tab())
+      link_ids <- result[[1]]
+      gene_name <- result[[2]]
+      selected_gene_name(gene_name)
+    
+      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)))
+                    
+    })
+    
+    
+    observeEvent(input$sankey_box$maximized, {
+      plot_height <- if (input$sankey_box$maximized) {
+        "100%"
+      } else {
+        "50vh"
+      }
+      
+      js_call <- sprintf(
+        "
+      setTimeout(() => {
+        $('#%s').css('height', '%s');
+      }, 500)
+      $('#%s').trigger('resize');
+      ",
+      "app-sankey-sankey_plt",
+      plot_height,
+      "app-sankey-sankey_plt"
+      )
+      shinyjs::runjs(js_call)
+    }, ignoreInit = TRUE)
+    
+    return(selected_gene_name)
+  })
+}
+
+
+#' sankey_link_selection
+#'
+#' @param click_data 
+#' @param path_gene_tab 
+#' @param gene_variant_tab 
+#'
+#' @return
+#' @export
+#'
+#' @examples
+sankey_link_selection <- function(click_data, path_gene_tab, gene_variant_tab) {
+  clicked_link <- click_data$pointNumber + 1
+  
+  if (clicked_link <= nrow(path_gene_tab)) {
+    return(first_level_link_selection(clicked_link, path_gene_tab, gene_variant_tab))
+  } 
+  return(second_level_link_selection(clicked_link, path_gene_tab, gene_variant_tab))
+}
+
+
+#' first_level_link_selection
+#'
+#' @param clicked_link 
+#' @param path_gene_tab 
+#' @param gene_variant_tab 
+#'
+#' @return
+#' @export
+#'
+#' @examples
+first_level_link_selection <- function(clicked_link, path_gene_tab, gene_variant_tab) {
+  select_gene_name <- path_gene_tab[clicked_link]$gene_name
+  labels <- data.table(label = c(path_gene_tab$kegg_paths_name, gene_variant_tab$gene_name), id = c(path_gene_tab$first, gene_variant_tab$second))
+  first_links <- clicked_link
+
+  second_links <- which(labels$label == select_gene_name)
+  link_ids <- unique(c(
+    first_links,
+    second_links)
+  )
+  return(list(link_ids, select_gene_name))
+}
+
+
+#' second_level_link_selection
+#'
+#' @param clicked_link 
+#' @param path_gene_tab 
+#' @param gene_variant_tab 
+#'
+#' @return
+#' @export
+#'
+#' @examples
+second_level_link_selection <- function(clicked_link, path_gene_tab, gene_variant_tab) {
+  select_gene_name <- gene_variant_tab[(clicked_link - nrow(path_gene_tab))]$gene_name
+  labels <- data.table(label = c(path_gene_tab$kegg_paths_name, gene_variant_tab$gene_name), id = c(path_gene_tab$first, gene_variant_tab$second))
+  
+  first_links <- which(path_gene_tab$gene_name == select_gene_name) 
+  second_links <- which(labels$label == select_gene_name)
+
+  link_ids <- unique(c(
+    first_links,
+    second_links)
+  )
+  return(list(link_ids, select_gene_name))
+}
+
+

app/view/table.R

@@ -0,0 +1,162 @@
+box::use(
+  shiny[moduleServer, req, NS, observeEvent, tagList, reactiveVal, h3, div, reactive, HTML],
+  bs4Dash[actionButton, useAutoColor, box],
+  DT[renderDataTable, dataTableOutput],
+  gargoyle[trigger]
+)
+
+box::use(
+  app/logic/render_table[render_pathways_table, render_genes_table]
+)
+
+
+
+#' @export
+ui <- function(id) {
+  ns <- NS(id)
+  tagList(
+    box(
+      solidHeader = TRUE,
+      title = div(
+        class = "header-btns",
+        bs4Dash::actionButton(
+          ns("reset_btn"),
+          label = "Reset selection",
+          status = "secondary"
+        ),
+        HTML(
+          '
+                  <div id="feat-radio" style="margin-left: 15px" class="feat-radio-container">
+                    <h4>Pathway</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>
+                  </div>
+
+                  <script>
+
+                  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"});
+                    }
+                  });
+
+                  </script>
+
+              '
+        )
+      ),
+      collapsible = TRUE,
+      status = "navy",
+      width = 12,
+      dataTableOutput(ns("table"), height = "40%")
+    )
+  )
+
+}
+
+#' @export
+server <- function(id, data) {
+  
+  moduleServer(id, function(input, output, session) {
+    is_path_tab_active <- reactiveVal(TRUE)
+    selected_pathways <- reactiveVal(NULL)
+    selected_genes <- reactiveVal(NULL)
+    
+    pathways_tab <- reactive({
+      tab <- unique(data[, .(kegg_paths_name)])
+      colnames(tab) <- "pathway"
+      return(tab)
+    })
+    
+    genes_tab <- reactive({
+      unique(data[, .(gene_name)])
+    })
+    
+    observeEvent(pathways_tab(),{
+      req(pathways_tab())
+      output$table <- render_pathways_table(
+        pathways_tab(),
+        selected_pathways()
+      )
+    })
+
+    
+    observeEvent(input$feature_radio, {
+      if (input$feature_radio == "gene") {
+        if (is_path_tab_active()) {
+          is_path_tab_active(FALSE)
+          output$table <- render_genes_table(
+            genes_tab(),
+            selected_genes()$row_i
+          )
+        }
+
+      } else if (input$feature_radio == "pathway") {
+        if (!(is_path_tab_active())) {
+          is_path_tab_active(TRUE)
+          output$table <- render_pathways_table(
+            pathways_tab(),
+            selected_pathways()$row_i
+          )
+          
+        }
+      }
+      
+    })
+    
+    
+    observeEvent(input$reset_btn, {
+      if ((is_path_tab_active())) {
+        selected_pathways(NULL)
+        output$table <- render_pathways_table(
+          pathways_tab()
+        )
+        trigger("reset_sankey")
+        
+      }
+      else {
+        selected_genes(NULL)
+        output$table <- render_genes_table(
+          genes_tab()
+        )
+      }
+      
+      
+    })
+    
+    
+    ############# FEATURE SELECTION ##########
+    observeEvent(input$table_cell_clicked, {
+      gene <- input$table_cell_clicked[["value"]]
+      row <- input$table_cell_clicked[["row"]]
+      req(gene)
+      if (is.null(row)) {
+        print("it is null")
+        return(NULL)
+      }
+      
+      rows <- input$table_rows_selected
+      if (is_path_tab_active()) {
+        features <- pathways_tab()[rows]
+        features[, row_i := rows]
+        selected_pathways(features)
+      } else {
+        features <- genes_tab()[rows]
+        features[, row_i := rows]
+        selected_genes(features)
+      }
+      print(selected_pathways())
+    })
+    
+    return(reactiveVal(list(selected_pathways, selected_genes, is_path_tab_active)))
+  })
+}
+
+
+