Merge pull request #30 from allaway/drug-selector

Drug selector

R/mod_cell_line_selector.R

@@ -0,0 +1,58 @@
+#' cell_line_selector UI Function
+#'
+#' @description A shiny Module.
+#'
+#' @param id,input,output,session Internal parameters for {shiny}.
+#'
+#' @noRd 
+#'
+#' @importFrom shiny NS tagList 
+mod_cell_line_selector_ui <- function(id){
+  ns <- NS(id)
+  tagList(
+    box(
+      column(checkboxGroupInput(ns("nf1_genotypes"),label = "NF1 Genotype", choices = unique(kairos::drug_screening$nf1Genotype),
+                                selected =  unique(kairos::drug_screening$nf1Genotype)),
+             width = 2),
+      column(checkboxGroupInput(ns("nf2_genotypes"),label = "NF2 Genotype", choices = unique(kairos::drug_screening$nf2Genotype),
+                                selected =  unique(kairos::drug_screening$nf2Genotype)),
+             width = 2),
+             checkboxGroupInput(ns("nf2_knockdowns"),label = "NF1 Knockdowns", choices = unique(kairos::drug_screening$nf1Knockdown),
+                                selected =  unique(kairos::drug_screening$nf1Knockdown)),
+             checkboxGroupInput(ns("nf2_knockdowns"),label = "NF2 Knockdowns", choices = unique(kairos::drug_screening$nf2Knockdown),
+                                selected =  unique(kairos::drug_screening$nf2Knockdown)),
+  width = 12),
+  box("Selected Cell Lines:",
+    DT::dataTableOutput(ns("cell_lines_table")),
+  width = 12)
+  )
+}
+
+#' cell_line_selector Server Function
+#'
+#' @noRd 
+mod_cell_line_selector_server <- function(input, output, session){
+  ns <- session$ns
+
+  models <- reactive({
+    kairos::drug_screening %>% 
+    dplyr::select(model_name, disease_name, symptom_name, nf1Genotype, nf2Genotype, nf1Knockdown, nf2Knockdown) %>% 
+    dplyr::distinct()
+  })
+
+  output$cell_lines_table <- DT::renderDataTable({
+    models() %>% dplyr::filter(nf1Genotype %in% input$nf1_genotypes,
+                                  nf2Genotype %in% input$nf2_genotypes)
+  })
+
+  cell_lines <- reactive({models() %>% 
+                                purrr::pluck('model_name') %>% 
+                                unique()})
+}
+
+## To be copied in the UI
+# mod_cell_line_selector_ui("cell_line_selector_ui_1")
+
+## To be copied in the server
+# callModule(mod_cell_line_selector_server, "cell_line_selector_ui_1")
+

R/mod_compound_selector.R

@@ -0,0 +1,30 @@
+#' compound_selector UI Function
+#'
+#' @description A shiny Module.
+#'
+#' @param id,input,output,session Internal parameters for {shiny}.
+#'
+#' @noRd 
+#'
+#' @importFrom shiny NS tagList 
+mod_compound_selector_ui <- function(id){
+  ns <- NS(id)
+  tagList(
+
+  )
+}
+
+#' compound_selector Server Function
+#'
+#' @noRd 
+mod_compound_selector_server <- function(input, output, session){
+  ns <- session$ns
+
+}
+
+## To be copied in the UI
+# mod_compound_selector_ui("compound_selector_ui_1")
+
+## To be copied in the server
+# callModule(mod_compound_selector_server, "compound_selector_ui_1")
+

R/mod_dose_response.R

@@ -17,7 +17,7 @@ mod_dose_response_ui <- function(id){
 #' dose_response Server Function
 #'
 #' @noRd 
-mod_dose_response_server <- function(input, output, session, cell_lines){
+mod_dose_response_server <- function(input, output, session, cell_lines, compounds){
   ns <- session$ns
 
 }

R/mod_drug_screening_page.R

@@ -26,25 +26,30 @@ mod_drug_screening_page_ui <- function(id){
                  icon = icon("pills")
         ),
         menuItem("Select Cell Lines",
-                 tabName = 'cohort',
+                 tabName = 'cell_lines',
                  icon = icon("wrench")
         ),
-        menuItem("Run Analyses",
-                 icon = icon("chart-area"), startExpanded = TRUE,
-                 menuSubItem(
-                   "Dose-Response",
+        menuItem("Select Compounds",
+                 tabName = 'compounds',
+                 icon = icon("wrench")
+        ),
+        menuItem("Dose-Response",
                    tabName = "dose_response",
                    icon = icon("cog")
-                 )))),
+                 ))),
       dashboardBody(
         tagList(
           tabItems(
             tabItem(
               tabName = "dashboard"
             ),
             tabItem(
-              tabName = 'cohort',
-              mod_cohort_page_ui(ns("cohort_page_ui_1"))
+              tabName = 'cell_lines',
+              mod_cell_line_selector_ui(ns("cell_line_selector_ui_1"))
+            ),
+            tabItem(
+              tabName = 'compounds',
+              mod_compound_selector_ui(ns("compound_selector_ui_1"))
             ),
             tabItem(
               tabName = 'dose_response',
@@ -64,8 +69,9 @@ mod_drug_screening_page_ui <- function(id){
 
 mod_drug_screening_page_server <- function(input, output, session){
   ns <- session$ns
-  cell_lines <- NULL
-  callModule(mod_dose_response_server, "dose_response_ui_1", cell_lines)
+  cell_lines <- callModule(mod_cell_line_selector_server, "cell_line_selector_ui_1")
+  compounds <-callModule(mod_compound_selector_server, "compound_selector_ui_1")
+  callModule(mod_dose_response_server, "dose_response_ui_1", cell_lines, compounds)
 }
 
 ## To be copied in the UI

data-raw/drug_screening.R

@@ -0,0 +1,18 @@
+## code to prepare `drug_screening` dataset goes here
+library(synapser)
+library(tidyverse)
+synLogin()
+
+drug_screening <- synGet("syn20700260")$path %>% readr::read_csv(
+  col_types = "cccccdcdccccdcdccdc"
+) 
+
+genotypes <- synTableQuery('select * from syn21830362', includeRowIdAndRowVersion = F)$filepath %>% 
+  read_csv() %>% 
+  rename(model_name = specimenID)
+
+drug_screening <- left_join(drug_screening, genotypes)
+
+usethis::use_data(drug_screening,
+                  #overwrite = T
+                  )