feat: dashboard filters working reactively

Oliversinn · Dec 15, 2023 · 0794595 · 0794595
1 parent a7ec779
commit 0794595
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Showing 5 changed files with 96 additions and 18 deletions.
diff --git a/Dashboard/global.R b/Dashboard/global.R
@@ -8,6 +8,15 @@ library(fontawesome)
 library(plotly)
 library(dplyr)
 library(htmltools)
+library(GenomicDataCommons)
+
+projects <- GenomicDataCommons::projects() %>%
+  GenomicDataCommons::filter(program.name == "TCGA") %>%
+  GenomicDataCommons::facet(c("name", "project_id")) %>%
+  results_all()
+
+tcga_project_ids_list <- projects$project_id
+tcga_project_ids_list <- c("TODOS", tcga_project_ids_list)
 
 
 Sys.setenv(OPENSSL_CONF = "/dev/null")

diff --git a/Dashboard/server.R b/Dashboard/server.R
@@ -1,3 +1,67 @@
 function(input, output, session) {
+  # Filters ---
+  ## projects_reactive ----
+  projects_reactive <- reactive({
+    projects <- GenomicDataCommons::projects() %>%
+      GenomicDataCommons::filter(program.name == "TCGA") %>%
+      GenomicDataCommons::facet(c("name", "project_id"))
 
+    if (input$project_id != "TODOS") {
+      projects <- projects %>%
+        GenomicDataCommons::filter(project_id == input$project_id)
+    }
+
+    if (input$disease_type != "TODOS") {
+      projects <- projects %>%
+        GenomicDataCommons::filter(disease_type == input$disease_type)
+    }
+
+    if (input$primary_site != "TODOS") {
+      projects <- projects %>%
+        GenomicDataCommons::filter(primary_site == input$primary_site)
+    }
+
+    projects <- projects %>%
+      GenomicDataCommons::results_all()
+  })
+
+  ## disease_type filter ----
+  diseases_types_reactive <- reactive({
+    unique(
+      rapply(projects_reactive()$disease_type, function(x) head(x, 100))
+    )
+  })
+
+  diseases_types_list <- reactive({
+    c("TODOS", diseases_types_reactive())
+  })
+
+  observe({
+    updateSelectInput(
+      session,
+      "disease_type",
+      choices = diseases_types_list(),
+      selected = input$disease_type
+    )
+  })
+
+  # primary_site filter ----
+  primary_site_reactive <- reactive({
+    unique(
+      rapply(projects_reactive()$primary_site, function(x) head(x, 100))
+    )
+  })
+
+  primary_site_list <- reactive({
+    c("TODOS", primary_site_reactive())
+  })
+
+  observe({
+    updateSelectInput(
+      session,
+      "primary_site",
+      choices = primary_site_list(),
+      selected = input$primary_site
+    )
+  })
 }
diff --git a/Dashboard/ui.R b/Dashboard/ui.R
@@ -38,33 +38,33 @@ fluidPage(
         ### project_id ----
         selectInput(
           "project_id",
-          label = "Poject ID",
-          choices = c("Project 1", "Project 2"),
-          selected = "Project 1"
+          label = "Proyecto",
+          choices = tcga_project_ids_list,
+          selected = tcga_project_ids_list[1]
         ),
         bsTooltip(
           "project_id",
           "Seleccionar un proyecto",
           placement = "right", trigger = "hover", options = NULL
         ),
-        ### primary_diagnosis ----
+        ### disease_type ----
         selectInput(
-          "primary_diagnosis",
-          label = "Primary diagnosis",
-          choices = c("Diagnosis 1", "Diagnosis 2"),
-          selected = "Diagnosis 1"
+          "disease_type",
+          label = "Tipo de enfermedad",
+          choices = c("TODOS"),
+          selected = "TODOS"
         ),
         bsTooltip(
-          "primary_diagnosis",
-          "Seleccionar un primary diagnosis",
+          "disease_type",
+          "Seleccionar un tipo de enfermedad",
           placement = "right", trigger = "hover", options = NULL
         ),
         ### primary_site ----
         selectInput(
           "primary_site",
           label = "Primary site",
-          choices = c("Site 1", "Site 2"),
-          selected = "Site 1"
+          choices = c("TODOS"),
+          selected = "TODOS"
         ),
         bsTooltip(
           "primary_site",

diff --git a/setup.R b/setup.R
@@ -4,17 +4,21 @@ library(GenomicDataCommons)
 projects <- GenomicDataCommons::projects() %>%
   GenomicDataCommons::filter(program.name == "TCGA") %>%
   GenomicDataCommons::facet(c("name", "project_id")) %>%
-  results(size = 100)
+  results_all()
 
-tcga_project_ids <- projects$project_id
+tcga_project_ids_list <- projects$project_id
 
 projects_info <- projects() %>%
   GenomicDataCommons::filter(project_id %in% tcga_project_ids) %>%
   results_all()
 
-diseases_types <- unique(rapply(projects$disease_type, function(x) head(x, 30)))
+diseases_types <- unique(
+  rapply(projects$disease_type, function(x) head(x, 100))
+)
 
-primary_sites <- unique(rapply(projects$primary_site, function(x) head(x, 30)))
+primary_sites <- unique(
+  rapply(projects$primary_site, function(x) head(x, 100))
+)
 
 cases_pre_info <- cases() %>%
   GenomicDataCommons::filter(project.project_id %in% tcga_project_ids) %>%
@@ -37,5 +41,7 @@ cases_info <- GenomicDataCommons::cases() %>%
 
 files_info <- GenomicDataCommons::files() %>%
   GenomicDataCommons::filter(access == "open") %>%
-  GenomicDataCommons::facet(c("type", "data_type")) %>%
+  GenomicDataCommons::facet(
+    c("type", "data_type", "analysis.workflow_type")
+  ) %>%
   aggregations()
diff --git a/tests.R b/tests.R
@@ -19,7 +19,6 @@ ge_manifest <- files() %>%
   filter(cases.project.project_id == "TCGA-OV") %>%
   filter(type == "gene_expression") %>%
   filter(analysis.workflow_type == "STAR - Counts") %>%
-  filter(analysis.workflow_type == "STAR - Counts") %>%
   filter(access == "open") %>%
   manifest(size = 5)