framework

DESCRIPTION

@@ -19,8 +19,9 @@ Imports:
     htmltools,
     ggplot2,
     plotly,
-    shinydashboard
-RoxygenNote: 6.1.0
+    shinydashboard,
+    readr
+RoxygenNote: 7.0.2
 Suggests: 
     testthat (>= 2.1.0),
     knitr,

NAMESPACE

@@ -1,6 +1,36 @@
 # Generated by roxygen2: do not edit by hand
 
+export(includeRMarkdown)
+export(mod_about_page_server)
+export(mod_about_page_ui)
+export(mod_cohort_display_server)
+export(mod_cohort_display_ui)
+export(mod_cohort_page_server)
+export(mod_cohort_page_ui)
+export(mod_cohort_selector_server)
+export(mod_cohort_selector_ui)
+export(mod_docs_page_server)
+export(mod_docs_page_ui)
+export(mod_explore_body_server)
+export(mod_explore_body_ui)
+export(mod_explore_menu_server)
+export(mod_explore_menu_ui)
+export(mod_explore_page_server)
+export(mod_explore_page_ui)
+export(mod_resources_page_server)
+export(mod_resources_page_ui)
 export(run_app)
 import(shiny)
+import(shinydashboard)
+importFrom(glue,glue)
 importFrom(golem,with_golem_options)
+importFrom(htmltools,HTML)
+importFrom(htmltools,tagAppendAttributes)
+importFrom(htmltools,tagList)
+importFrom(htmltools,tags)
+importFrom(markdown,markdownToHTML)
+importFrom(rmarkdown,render)
+importFrom(shiny,NS)
+importFrom(shiny,column)
 importFrom(shiny,shinyApp)
+importFrom(shiny,tagList)

R/app_server.R

@@ -2,5 +2,9 @@
 #' @import shinydashboard
 
 app_server <- function(input, output,session) {
-  callModule(mod_cohort_server, "cohort_ui_1")
+  callModule(mod_cohort_page_server, "cohort_page_ui_1")
+  callModule(mod_explore_page_server, "explore_page_ui_1")
+  callModule(mod_docs_page_server, "docs_page_ui_1")
+  callModule(mod_about_page_server, "about_page_ui_1")
+  callModule(mod_resources_page_server, "resources_page_ui_1")
 }

R/app_ui.R

@@ -5,14 +5,25 @@ app_ui <- function() {
   tagList(
     # Leave this function for adding external resources
     golem_add_external_resources(),
-    # List the first level UI elements here 
-    kashboardPage(
-      dashboardHeader(),
-      dashboardSidebar(
-        mod_cohort_ui("cohort_ui_1")
-      ),
-      dashboardBody()
-    )
+    navbarPage(    
+      title = strong("kairos"), selected = "Cohort Builder",	
+      tabPanel("Cohort Builder",
+               mod_cohort_page_ui("cohort_page_ui_1"),
+               icon = icon("wrench")),
+      tabPanel("Explore",
+               mod_explore_page_ui("explore_page_ui_1"),
+               icon = icon("chart-area")),	
+      tabPanel("Documentation",
+               mod_docs_page_ui("docs_page_ui_1"),
+               icon = icon("book-reader")),	
+      tabPanel("About",
+               mod_about_page_ui("about_page_ui_1"),
+               icon = icon("info-circle")),	
+      tabPanel("Resources",
+               mod_resources_page_ui("resources_page_ui_1"),
+               icon = icon("external-link")),
+      collapsible = TRUE,	inverse = TRUE,
+      windowTitle = "kairos")
   )
 }
 
@@ -25,10 +36,10 @@ golem_add_external_resources <- function(){
 
   tags$head(
     golem::activate_js(),
-    golem::favicon()
+    golem::favicon(),
     # Add here all the external resources
     # If you have a custom.css in the inst/app/www
     # Or for example, you can add shinyalert::useShinyalert() here
-    #tags$link(rel="stylesheet", type="text/css", href="www/custom.css")
+    tags$link(rel="stylesheet", type="text/css", href="www/custom.css")
   )
 }

R/mod_about_page.R

@@ -0,0 +1,38 @@
+# Module UI
+
+#' @title   mod_about_page_ui and mod_about_page_server
+#' @description  A shiny Module.
+#'
+#' @param id shiny id
+#' @param input internal
+#' @param output internal
+#' @param session internal
+#'
+#' @rdname mod_about_page
+#'
+#' @keywords internal
+#' @export 
+#' @importFrom shiny NS tagList 
+mod_about_page_ui <- function(id){
+  ns <- NS(id)
+  tagList(
+
+  )
+}
+
+# Module Server
+
+#' @rdname mod_about_page
+#' @export
+#' @keywords internal
+
+mod_about_page_server <- function(input, output, session){
+  ns <- session$ns
+}
+
+## To be copied in the UI
+# mod_about_page_ui("about_page_ui_1")
+
+## To be copied in the server
+# callModule(mod_about_page_server, "about_page_ui_1")
+

R/mod_cohort_display.R

@@ -0,0 +1,35 @@
+# Module UI
+
+#' @title   mod_cohort_display_ui and mod_cohort_display_server
+#' @description  A shiny Module.
+#'
+#' @param id shiny id
+#' @param input internal
+#' @param output internal
+#' @param session internal
+#'
+#' @rdname mod_cohort_display
+#'
+#' @keywords internal
+#' @export 
+#' @importFrom shiny NS tagList 
+mod_cohort_display_ui <- function(id){
+  ns <- NS(id)
+}
+
+# Module Server
+
+#' @rdname mod_cohort_display
+#' @export
+#' @keywords internal
+
+mod_cohort_display_server <- function(input, output, session){
+  ns <- session$ns
+}
+
+## To be copied in the UI
+# mod_cohort_display_ui("cohort_display_ui_1")
+
+## To be copied in the server
+# callModule(mod_cohort_display_server, "cohort_display_ui_1")
+

R/mod_cohort_page.R

@@ -0,0 +1,68 @@
+# Module UI
+
+#' @title   mod_cohort_page_ui and mod_cohort_page_server
+#' @description  A shiny Module.
+#'
+#' @param id shiny id
+#' @param input internal
+#' @param output internal
+#' @param session internal
+#'
+#' @rdname mod_cohort_page
+#'
+#' @keywords internal
+#' @export 
+#' @importFrom shiny NS tagList 
+mod_cohort_page_ui <- function(id){
+  ns <- NS(id)
+  tagList(
+    dashboardPage(
+      dashboardHeader(disable = T),
+      dashboardSidebar(
+          checkboxGroupInput(ns('isCellLine'), label = "Is Cell Line", choices = unique(cohort$isCellLine), 
+                             selected = unique(cohort$isCellLine)),
+          checkboxGroupInput(ns("tumorType"), label = "Tumor Type", choices = unique(cohort$tumorType),
+                              selected =  unique(cohort$tumorType)),
+          checkboxGroupInput(ns("species"), label = "Species", choices = unique(cohort$species), 
+                              selected = unique(cohort$species)),
+          selectizeInput(ns("studyName"), label = "Study Name", choices = unique(cohort$studyName),
+                          selected = unique(cohort$studyName), multiple = T)),
+      dashboardBody(
+          box(width = 12, div(DT::dataTableOutput(ns('data_table')))),
+    )))
+}
+
+# Module Server
+
+#' @rdname mod_cohort_page
+#' @export
+#' @keywords internal
+
+mod_cohort_page_server <- function(input, output, session){
+  ns <- session$ns
+
+  output$data_table <- DT::renderDataTable({
+    kairos::cohort %>%
+      dplyr::filter(studyName %in% input$studyName,
+                    isCellLine %in% input$isCellLine,
+                    tumorType %in% input$tumorType,
+                    species %in% input$species)  # kairos::cohort
+  })
+
+  output$specimens <- reactive({
+    kairos::cohort %>%
+      dplyr::filter(studyName %in% input$studyName,
+                    isCellLine %in% input$isCellLine,
+                    tumorType %in% input$tumorType,
+                    species %in% input$species) %>% 
+      purrr::pluck("specimenID") %>% 
+      unique()
+  })
+}
+
+## To be copied in the UI
+# mod_cohort_page_ui("cohort_page_ui_1")
+
+## To be copied in the server
+# callModule(mod_cohort_page_server, "cohort_page_ui_1")
+

R/mod_cohort_selector.R

@@ -0,0 +1,69 @@
+# Module UI
+
+#' @title   mod_cohort_selector_ui and mod_cohort_selector_server
+#' @description  A shiny Module.
+#'
+#' @param id shiny id
+#' @param input internal
+#' @param output internal
+#' @param session internal
+#'
+#' @rdname mod_cohort_selector
+#'
+#' @keywords internal
+#' @export 
+#' @importFrom shiny NS tagList 
+mod_cohort_selector_ui <- function(id){
+  ns <- NS(id)
+  tagList(
+    # actionButton(ns('button'), label = "Build!"),
+    checkboxGroupInput(ns('isCellLine'), label = "Is Cell Line", choices = unique(cohort$isCellLine), 
+                       selected = unique(cohort$isCellLine)),
+    # ,
+    # checkboxGroupInput(ns("tumorType"), label = "Tumor Type", choices = unique(cohort$tumorType),
+    #                    selected =  unique(cohort$tumorType)),
+    # checkboxGroupInput(ns("species"), label = "Species", choices = unique(cohort$species), 
+    #                    selected = unique(cohort$species)),
+    # selectizeInput(ns("modelSystemName"), label = "Model System Name", choices = unique(cohort$modelSystemName), 
+    #                selected = unique(cohort$modelSystemName), multiple = T),
+    # selectizeInput(ns("studyName"), label = "Study Name", choices = unique(cohort$studyName),
+    #                selected = unique(cohort$studyName), multiple = T)
+    textOutput(ns("foo"))
+
+  )
+
+}
+
+# Module Server
+
+#' @rdname mod_cohort_selector
+#' @export
+#' @keywords internal
+
+mod_cohort_selector_server <- function(input, output, session){
+  ns <- session$ns
+
+ foo <- renderText(paste0("You have chosen: ", input$isCellLine))
+
+
+  # output$specimens <- reactive(input$isCellLine, {
+  #   print(input$isCellLine) 
+  #   kairos::cohort %>%
+  #     dplyr::filter(#studyName %in% input$studyName,
+  #                   # modelSystemName %in% input$modelSystemName,
+  #                    isCellLine %in% input$isCellLine
+  #                   # ,
+  #                   # tumorType %in% input$tumorType,
+  #                   # species %in% input$species
+  #                   ) %>%
+  #     purrr::pluck("specimenID") %>%
+  #     unique() })
+
+ }
+
+## To be copied in the UI
+# mod_cohort_selector_ui("cohort_selector_ui_1")
+
+## To be copied in the server
+# callModule(mod_cohort_selector_server, "cohort_selector_ui_1")
+

R/mod_cohort.R → R/mod_docs_page.R

@@ -1,19 +1,19 @@
 # Module UI
 
-#' @title   mod_cohort_ui and mod_cohort_server
+#' @title   mod_docs_page_ui and mod_docs_page_server
 #' @description  A shiny Module.
 #'
 #' @param id shiny id
 #' @param input internal
 #' @param output internal
 #' @param session internal
 #'
-#' @rdname mod_cohort
+#' @rdname mod_docs_page
 #'
 #' @keywords internal
 #' @export 
 #' @importFrom shiny NS tagList 
-mod_cohort_ui <- function(id){
+mod_docs_page_ui <- function(id){
   ns <- NS(id)
   tagList(
 
@@ -22,17 +22,17 @@ mod_cohort_ui <- function(id){
 
 # Module Server
 
-#' @rdname mod_cohort
+#' @rdname mod_docs_page
 #' @export
 #' @keywords internal
 
-mod_cohort_server <- function(input, output, session){
+mod_docs_page_server <- function(input, output, session){
   ns <- session$ns
 }
 
 ## To be copied in the UI
-# mod_cohort_ui("cohort_ui_1")
+# mod_docs_page_ui("docs_page_ui_1")
 
 ## To be copied in the server
-# callModule(mod_cohort_server, "cohort_ui_1")
+# callModule(mod_docs_page_server, "docs_page_ui_1")