board.drugconnectivity: inputData + ngs -> pgx

bigomics · Mar 14, 2023 · ff18b5e · ff18b5e
1 parent 1b0850c
commit ff18b5e
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Showing 6 changed files with 7 additions and 13 deletions.
diff --git a/components/app/R/server.R b/components/app/R/server.R
@@ -224,7 +224,7 @@ app_server <- function(input, output, session) {
 
           if(ENABLED['drug']) {
             info("[server.R] calling DrugConnectivityBoard module")
-            DrugConnectivityBoard("drug", inputData = inputData)
+            DrugConnectivityBoard("drug", pgx = PGX)
           }
 
           if(ENABLED['isect']) {

diff --git a/components/board.drugconnectivity/R/drugconnectivity_plot_actmap.R b/components/board.drugconnectivity/R/drugconnectivity_plot_actmap.R
@@ -124,7 +124,6 @@ drugconnectivity_plot_actmap_server <- function(id,
       }
 
       plot_data <- shiny::reactive({
-        pgx <- pgx()
         dsea_contrast <- dsea_contrast()
         dsea_method <- dsea_method()
         shiny::req(pgx, dsea_contrast, dsea_method)

diff --git a/components/board.drugconnectivity/R/drugconnectivity_plot_cmap_dsea.R b/components/board.drugconnectivity/R/drugconnectivity_plot_cmap_dsea.R
@@ -210,7 +210,7 @@ drugconnectivity_plot_cmap_dsea_server <- function(id,
 
       plot_data <- shiny::reactive({
         res <- list(
-          pgx = pgx(),
+          pgx = pgx,
           dsea = getActiveDSEA(),
           cmap_table = cmap_table,
           moa.class = getMOA.class(),

diff --git a/components/board.drugconnectivity/R/drugconnectivity_plot_cmap_enplot.R b/components/board.drugconnectivity/R/drugconnectivity_plot_cmap_enplot.R
@@ -49,7 +49,6 @@ drugconnectivity_plot_cmap_enplot_server <- function(id,
   moduleServer(
     id, function(input, output, session) {
       plot_data <- shiny::reactive({
-        pgx <- pgx()
         dsea <- getActiveDSEA()
 
         res <- list(

diff --git a/components/board.drugconnectivity/R/drugconnectivity_plot_enplots.R b/components/board.drugconnectivity/R/drugconnectivity_plot_enplots.R
@@ -54,7 +54,6 @@ drugconnectivity_plot_enplots_server <- function(id,
   moduleServer(
     id, function(input, output, session) {
       plot_data <- shiny::reactive({
-        pgx <- pgx()
         dsea_contrast <- dsea_contrast()
         dsea_method <- dsea_method()
         shiny::req(pgx, dsea_contrast, dsea_method)

diff --git a/components/board.drugconnectivity/R/drugconnectivity_server.R b/components/board.drugconnectivity/R/drugconnectivity_server.R
@@ -3,7 +3,7 @@
 ## Copyright (c) 2018-2022 BigOmics Analytics Sagl. All rights reserved.
 ##
 
-DrugConnectivityBoard <- function(id, inputData) {
+DrugConnectivityBoard <- function(id, pgx) {
   moduleServer(id, function(input, output, session) {
     ns <- session$ns ## NAMESPACE
 
@@ -24,7 +24,6 @@ DrugConnectivityBoard <- function(id, inputData) {
         allowfullscreen></iframe></center>")
 
     shiny::observe({
-      pgx <- inputData()
       shiny::req(pgx)
       ct <- names(pgx$drugs)
       shiny::updateSelectInput(session, "dsea_method", choices = ct)
@@ -43,7 +42,6 @@ DrugConnectivityBoard <- function(id, inputData) {
     })
 
     shiny::observe({
-      pgx <- inputData()
       shiny::req(pgx)
       ct <- colnames(pgx$model.parameters$contr.matrix)
       shiny::updateSelectInput(session, "dsea_contrast", choices = sort(ct))
@@ -55,7 +53,6 @@ DrugConnectivityBoard <- function(id, inputData) {
 
     # common getData-esque function for drug connectivity plots / tables
     getActiveDSEA <- shiny::reactive({
-      pgx <- inputData()
       shiny::req(pgx, input$dsea_contrast, input$dsea_method)
 
       contr <- input$dsea_contrast
@@ -164,7 +161,7 @@ DrugConnectivityBoard <- function(id, inputData) {
     ## --------- DSEA enplot plotting module
     drugconnectivity_plot_enplots_server(
       "dsea_enplots",
-      inputData,
+      pgx,
       reactive(input$dsea_contrast),
       reactive(input$dsea_method),
       dsea_table,
@@ -184,7 +181,7 @@ DrugConnectivityBoard <- function(id, inputData) {
     ## -------- Activation map plotting module
     drugconnectivity_plot_actmap_server(
       "dsea_actmap",
-      inputData,
+      pgx,
       reactive(input$dsea_contrast),
       reactive(input$dsea_method),
       dsea_table,
@@ -204,15 +201,15 @@ DrugConnectivityBoard <- function(id, inputData) {
 
     drugconnectivity_plot_cmap_enplot_server(
       "cmap_enplot",
-      inputData,
+      pgx,
       getActiveDSEA,
       cmap_table,
       watermark = WATERMARK
     )
 
     drugconnectivity_plot_cmap_dsea_server(
       "cmap_dsea",
-      pgx = inputData,
+      pgx = pgx,
       getActiveDSEA = getActiveDSEA,
       cmap_table = cmap_table,
       getMOA.class = getMOA.class,