cohort builder first pass

DESCRIPTION

@@ -19,8 +19,9 @@ Imports:
     htmltools,
     ggplot2,
     plotly,
-    shinydashboard
-RoxygenNote: 6.1.0
+    shinydashboard,
+    readr
+RoxygenNote: 7.0.1
 Suggests: 
     testthat (>= 2.1.0),
     knitr,

NAMESPACE

@@ -1,6 +1,20 @@
 # Generated by roxygen2: do not edit by hand
 
+export(includeRMarkdown)
+export(mod_cohort_server)
+export(mod_cohort_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_ui.R

@@ -6,7 +6,7 @@ app_ui <- function() {
     # Leave this function for adding external resources
     golem_add_external_resources(),
     # List the first level UI elements here 
-    kashboardPage(
+    dashboardPage(
       dashboardHeader(),
       dashboardSidebar(
         mod_cohort_ui("cohort_ui_1")

R/mod_cohort.R

@@ -16,7 +16,16 @@
 mod_cohort_ui <- function(id){
   ns <- NS(id)
   tagList(
-
+    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)
   )
 }
 
@@ -28,6 +37,18 @@ mod_cohort_ui <- function(id){
 
 mod_cohort_server <- function(input, output, session){
   ns <- session$ns
+
+  samples <- reactive({
+    cohort %>% 
+      dplyr::filter(studyName %in% input$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

data-raw/cohort.R

@@ -0,0 +1,4 @@
+## code to prepare `cohort` dataset goes here
+
+cohort <- readr::read_csv("data-raw/cohort_metadata.csv")
+usethis::use_data(cohort)