feat: resection_site and primary_diagnosis added

Oliversinn · Dec 16, 2023 · ce46770 · ce46770
1 parent fc670b9
commit ce46770
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Showing 4 changed files with 124 additions and 13 deletions.
diff --git a/Dashboard/explorer.R b/Dashboard/explorer.R
@@ -62,7 +62,7 @@ project_id_dt <- function(data) {
   return(data)
 }
 
-primary_site_barplot <- function(data, variable_name) {
+aggregation_substr_barplot <- function(data, variable_name) {
   data <- as.data.frame(data)
 
   xticks_labels <- as.list(substr(data$key, 1, 30))

diff --git a/Dashboard/global.R b/Dashboard/global.R
@@ -13,15 +13,6 @@ library(DT)
 library(BiocManager)
 options(repos = BiocManager::repositories())
 
-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")
 options(shiny.fullstacktrace = TRUE)
 

diff --git a/Dashboard/server.R b/Dashboard/server.R
@@ -1,4 +1,12 @@
 function(input, output, session) {
+  # Static data ----
+  projects <- GenomicDataCommons::projects() %>%
+    GenomicDataCommons::filter(program.name == "TCGA") %>%
+    GenomicDataCommons::facet(c("name", "project_id")) %>%
+    results_all()
+
+  tcga_project_ids_list <- projects$project_id
+  tcga_project_ids_list <- c("TODOS", tcga_project_ids_list)
   # Filters ---
   ## projects_reactive ----
   projects_reactive <- reactive({
@@ -123,7 +131,7 @@ function(input, output, session) {
   ## primary_site ----
   ### barplot ----
   output$primary_site_barplot <- renderPlotly({
-    primary_site_barplot(
+    aggregation_substr_barplot(
       head(explorer_data_reactive()$primary_site, 30),
       "Sitio primario"
     )
@@ -138,6 +146,42 @@ function(input, output, session) {
     )
   })
 
+  ## primary_diagnosis ----
+  ### barplot ----
+  output$primary_diagnosis_barplot <- renderPlotly({
+    aggregation_substr_barplot(
+      head(explorer_data_reactive()$diagnoses.primary_diagnosis, 30),
+      "Diagnóstico primario"
+    )
+  })
+
+  ### datatable ----
+  output$primary_diagnosis_dt <- renderDataTable({
+    aggregation_dt(
+      explorer_data_reactive()$diagnoses.primary_diagnosis,
+      "Diagnóstico primario",
+      "casos_por_diagnostico_primario"
+    )
+  })
+
+  ## site_of_resection_or_biopsy ----
+  ### barplot ----
+  output$resection_site_barplot <- renderPlotly({
+    aggregation_substr_barplot(
+      head(explorer_data_reactive()$diagnoses.site_of_resection_or_biopsy, 30),
+      "Sitio de Resección o Biopsia"
+    )
+  })
+
+  ### datatable ----
+  output$resection_site_dt <- renderDataTable({
+    aggregation_dt(
+      explorer_data_reactive()$diagnoses.site_of_resection_or_biopsy,
+      "Sitio de Resección o Biopsia",
+      "casos_por_sitio_de_reseccion_o_biopsia"
+    )
+  })
+
   ## race ----
   ### barplot ----
   output$race_barplot <- renderPlotly({
@@ -186,7 +230,7 @@ function(input, output, session) {
   output$gender_dt <- renderDataTable({
     aggregation_dt(
       explorer_data_reactive()$demographic.gender,
-      "Genero",
+      "Género",
       "casos_por_genero"
     )
   })

diff --git a/Dashboard/ui.R b/Dashboard/ui.R
@@ -92,7 +92,9 @@ fluidPage(
           ## Tab EXPLORADOR ----
           tabItem(
             tabName = "EXPLORADOR",
-            h2("Explorador de datos"),
+            h1("Explorador de datos"),
+            br(),
+            h2("Proyectos"),
             br(),
             fluidRow(
               width = 12,
@@ -163,6 +165,80 @@ fluidPage(
                 )
               )
             ),
+            fluidRow(
+              width = 12,
+              ### primary_diagnosis ----
+              box(
+                width = 6,
+                solidHeader = TRUE,
+                collapsible = TRUE,
+                title = "Número de casos por diagnóstico primario",
+                tabBox(
+                  width = 12,
+                  height = NULL,
+                  #### barplot ----
+                  tabPanel(
+                    title = "Gráfico de barras",
+                    icon = icon("chart-bar"),
+                    h4(
+                      class = "text-center",
+                      "Número de Casos por Diagnóstico Primario (top 30)"
+                    ),
+                    shinycssloaders::withSpinner(
+                      plotlyOutput("primary_diagnosis_barplot", height = 500),
+                      color = "#1c9ad6", type = "8", size = 0.5
+                    )
+                  ),
+                  #### datatable ----
+                  tabPanel(
+                    title = "Cuadro de datos",
+                    icon = icon("table"),
+                    shinycssloaders::withSpinner(
+                      dataTableOutput("primary_diagnosis_dt"),
+                      color = "#1c9ad6", type = "8", size = 0.5
+                    )
+                  )
+                )
+              ),
+              ### site_of_resection_or_biopsy ----
+              box(
+                width = 6,
+                solidHeader = TRUE,
+                collapsible = TRUE,
+                title = "Número de casos por sitio de resección o biopsia",
+                tabBox(
+                  width = 12,
+                  height = NULL,
+                  #### barplot ----
+                  tabPanel(
+                    title = "Gráfico de barras",
+                    icon = icon("chart-bar"),
+                    h4(
+                      class = "text-center",
+                      paste0(
+                        "Número de Casos por ",
+                        "Sitio de Resección o Biopsia (top 30)"
+                      )
+                    ),
+                    shinycssloaders::withSpinner(
+                      plotlyOutput("resection_site_barplot", height = 500),
+                      color = "#1c9ad6", type = "8", size = 0.5
+                    )
+                  ),
+                  #### datatable ----
+                  tabPanel(
+                    title = "Cuadro de datos",
+                    icon = icon("table"),
+                    shinycssloaders::withSpinner(
+                      dataTableOutput("resection_site_dt"),
+                      color = "#1c9ad6", type = "8", size = 0.5
+                    )
+                  )
+                )
+              )
+            ),
+            h2("Demografía"),
+            br(),
             fluidRow(
               ### race ----
               box(