feat: added project plots and graphs

Dashboard/global.R

@@ -11,7 +11,7 @@ library(htmltools)
 library(GenomicDataCommons)
 library(DT)
 library(BiocManager)
-options(repos = BiocManager::repositories())
+# options(repos = BiocManager::repositories())
 load(file = "tcga.RData")
 tcga_project_ids_list <- c("TODOS", tcga_project_ids_list)
 
@@ -21,8 +21,13 @@ projects <- GenomicDataCommons::projects() %>%
   GenomicDataCommons::facet(c("name", "project_id")) %>%
   results_all()
 
+vb_style <- function(msg = '', style="font-size: 100%;") {
+  tags$p( msg , style = style )
+}
+
 
 Sys.setenv(OPENSSL_CONF = "/dev/null")
 options(shiny.fullstacktrace = TRUE)
 
 source("explorer.R")
+source("project.R")

Dashboard/project.R

@@ -0,0 +1,269 @@
+# project_disease_type_treemap ----
+project_disease_type_treemap <- function(data) {
+  project_disease_type_tree <- data %>% 
+    group_by(project_id, disease_type) %>% 
+    tally(name = "Casos") %>% 
+    mutate(
+      disease_type = paste(
+        Casos, disease_type
+      )
+    ) %>% 
+    rename(
+      "parent" = 1,
+      "label" = 2
+    )
+
+  project_disease_type_tree <- data %>% 
+    dplyr::select(project_id) %>% 
+    mutate(
+      parent = "Número de casos por proyecto y por tipo de enfermedad"
+    ) %>% 
+    group_by(parent, project_id) %>% 
+    tally(name = "Casos") %>% 
+    rename(
+      "parent" = 1,
+      "label" = 2
+    ) %>% 
+    rbind(., project_disease_type_tree) %>% 
+    replace(is.na(.), "Sin dato")
+
+  # project_disease_type_treemap ----
+  project_disease_type_treemap <- plot_ly(
+    data = project_disease_type_tree,
+    branchvalues = "total",
+    type = "treemap",
+    #ids = ~ids,
+    labels = ~label,
+    parents = ~parent,
+    values = ~Casos
+  )
+
+  return(project_disease_type_treemap)
+}
+
+project_disease_type_treedt <- function(data) {
+  data <- data %>% 
+    group_by(project_id, disease_type) %>% 
+    tally(name = "Número de casos", sort = TRUE) %>% 
+    rename(
+      "Proyecto" = 1,
+      "Tipo de enfermedad" = 2
+    ) %>% 
+    datatable(
+      extensions = "Buttons",
+      rownames = FALSE,
+      options = list(
+        language = list(
+          url = "//cdn.datatables.net/plug-ins/1.13.7/i18n/es-ES.json"
+        ),
+        dom = "Bfrtip",
+        buttons = list(
+          list(
+            extend = "csv",
+            filename = "casos_por_proyecto_tipo_enfermedad"
+          ),
+          list(
+            extend = "excel",
+            filename = "casos_por_proyecto_tipo_enfermedad"
+          )
+        ),
+        paging = FALSE,
+        scrollY = "400px",
+        scrollX = TRUE
+      )
+    )
+  return(data)
+}
+
+# project_bar ----
+project_bar <- function(data) {
+  fig <- data %>% 
+    group_by(project_id) %>% 
+    tally(name = "Número de casos", sort = TRUE) %>% 
+    rename("Proyecto" = 1) %>% 
+    plot_ly(
+      x = ~Proyecto, y = ~`Número de casos`, type = "bar"
+    ) %>%
+    layout(
+      xaxis = list(
+        title = "Proyecto",
+        categoryorder = "total descending"
+      ),
+      yaxis = list(
+        title = "Número de casos"
+      )
+    ) %>%
+    config(
+      displaylogo = FALSE,
+      modeBarButtonsToRemove = c(
+        "sendDataToCloud", "editInChartStudio", "pan2d", "select2d",
+        "drawclosedpath", "drawline", "drawrect", "drawopenpath",
+        "drawcircle", "eraseshape", "zoomIn2d", "zoomOut2d", "toggleSpikelines",
+        "lasso2d"
+      )
+    )
+  return(fig)
+}
+
+# project_bardt ----
+project_bardt <- function(data) {
+  data <- data %>% 
+    group_by(project_id, project_name) %>% 
+    tally(name = "Número de casos", sort = TRUE) %>% 
+    rename("Proyecto" = 1, "Nombre" = 2) %>% 
+    datatable(
+      extensions = "Buttons",
+      rownames = FALSE,
+      options = list(
+        language = list(
+          url = "//cdn.datatables.net/plug-ins/1.13.7/i18n/es-ES.json"
+        ),
+        dom = "Bfrtip",
+        buttons = list(
+          list(
+            extend = "csv",
+            filename = "casos_por_proyecto"
+          ),
+          list(
+            extend = "excel",
+            filename = "casos_por_proyecto"
+          )
+        ),
+        paging = FALSE,
+        scrollY = "400px",
+        scrollX = TRUE
+      )
+    )
+  return(data)
+}
+
+# disease_type_bar ----
+disease_type_bar <- function(data) {
+  fig <- data %>% 
+    group_by(disease_type) %>% 
+    tally(name = "Número de casos", sort = TRUE) %>% 
+    rename("Tipo de enfermedad" = 1) %>% 
+    plot_ly(
+      x = ~`Tipo de enfermedad`, y = ~`Número de casos`, type = "bar"
+    ) %>%
+    layout(
+      xaxis = list(
+        title = "Tipo de enfermedad",
+        categoryorder = "total descending"
+      ),
+      yaxis = list(
+        title = "Número de casos"
+      )
+    ) %>%
+    config(
+      displaylogo = FALSE,
+      modeBarButtonsToRemove = c(
+        "sendDataToCloud", "editInChartStudio", "pan2d", "select2d",
+        "drawclosedpath", "drawline", "drawrect", "drawopenpath",
+        "drawcircle", "eraseshape", "zoomIn2d", "zoomOut2d", "toggleSpikelines",
+        "lasso2d"
+      )
+    )
+  return(fig)
+}
+
+# disease_type_bardt ----
+disease_type_bardt <- function(data) {
+  data <- data %>% 
+    group_by(disease_type) %>% 
+    tally(name = "Número de casos", sort = TRUE) %>% 
+    rename("Tipo de enfermedad" = 1) %>% 
+    datatable(
+      extensions = "Buttons",
+      rownames = FALSE,
+      options = list(
+        language = list(
+          url = "//cdn.datatables.net/plug-ins/1.13.7/i18n/es-ES.json"
+        ),
+        dom = "Bfrtip",
+        buttons = list(
+          list(
+            extend = "csv",
+            filename = "casos_por_tipo_enfermedad"
+          ),
+          list(
+            extend = "excel",
+            filename = "casos_por_tipo_enfermedad"
+          )
+        ),
+        paging = FALSE,
+        scrollY = "400px",
+        scrollX = TRUE
+      )
+    )
+  return(data)
+}
+
+# primary_site_bar ----
+primary_site_bar <- function(data) {
+  data <- data %>% 
+    group_by(primary_site) %>% 
+    tally(name = "Número de casos", sort = TRUE) %>% 
+    rename("Sitio primario" = 1)
+
+  xticks_labels <- as.list(substr(data$`Sitio primario`, 1, 30))
+
+  fig <- plot_ly(
+      data,
+      x = ~`Sitio primario`, y = ~`Número de casos`, type = "bar"
+    ) %>%
+    layout(
+      xaxis = list(
+        title = "Sitio primario",
+        categoryorder = "total descending",
+        ticktext = xticks_labels,
+        tickvals = as.list(c(0:nrow(data))),
+        tickmode = "array"
+      ),
+      yaxis = list(
+        title = "Número de casos"
+      )
+    ) %>%
+    config(
+      displaylogo = FALSE,
+      modeBarButtonsToRemove = c(
+        "sendDataToCloud", "editInChartStudio", "pan2d", "select2d",
+        "drawclosedpath", "drawline", "drawrect", "drawopenpath",
+        "drawcircle", "eraseshape", "zoomIn2d", "zoomOut2d", "toggleSpikelines",
+        "lasso2d"
+      )
+    )
+  return(fig)
+}
+
+# primary_site_bardt ----
+primary_site_bardt <- function(data) {
+  data <- data %>% 
+    group_by(primary_site) %>% 
+    tally(name = "Número de casos", sort = TRUE) %>% 
+    rename("Sitio primario" = 1) %>% 
+    datatable(
+      extensions = "Buttons",
+      rownames = FALSE,
+      options = list(
+        language = list(
+          url = "//cdn.datatables.net/plug-ins/1.13.7/i18n/es-ES.json"
+        ),
+        dom = "Bfrtip",
+        buttons = list(
+          list(
+            extend = "csv",
+            filename = "casos_por_sitio_primario"
+          ),
+          list(
+            extend = "excel",
+            filename = "casos_por_sitio_primario"
+          )
+        ),
+        paging = FALSE,
+        scrollY = "400px",
+        scrollX = TRUE
+      )
+    )
+  return(data)
+}