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inst/shinyapp/PGdata.R

@@ -74,7 +74,7 @@ profile_vec_list$drug <- profile_vec_list$drug[!profile_vec_list$drug %in% c("OP
 ## clean OP*
 rm(list = ls()[grepl("OP", ls())])
 
-## some preprocess for Drugs-omics pairs analysis
+## some preprocess for Drug-Omics Correlation Analysis
 tmp <- list()
 
 tmp$omic_sel <- c("exp", "meth", "protein", "cnv")

inst/shinyapp/modules/07_PharmacoGenomics/DrugOmicPair.R

@@ -17,7 +17,7 @@ uiDrugOmicPair <- function(id){
       # Select omics ----
       column(4,
              selectizeInput(
-               ns("select_specific_omic"), "Molecule Selection:", choices = NULL,
+               ns("select_specific_omic"), "Molecule selection:", choices = NULL,
                options = list(
                  placeholder = 'Please select a molecular feature',
                  onInitialize = I('function() { this.setValue(""); }'), selected = "ABCC3"
@@ -27,7 +27,7 @@ uiDrugOmicPair <- function(id){
       # Select drugs ----
       column(4,
              selectizeInput(
-               ns("select_specific_drug"), "Drug Selection:", choices = NULL,
+               ns("select_specific_drug"), "Drug selection:", choices = NULL,
                options = list(
                  placeholder = 'Please select a drug',
                  onInitialize = I('function() { this.setValue(""); }'), selected = "YM-155"
@@ -66,15 +66,15 @@ serverDrugOmicPair <- function(input, output, session){
                                      "mutation_site" = omics_search[omics_search$type %in% "mutation_site",]$omics,
                                      "fusion" = omics_search[omics_search$type %in% "fusion",]$omics)
     updateSelectizeInput(session = session, inputId = 'select_specific_omic',
-                         label = 'Molecule Selection:', choices = omics_search_sel$omics, server = TRUE,
+                         label = 'Molecule selection:', choices = omics_search_sel$omics, server = TRUE,
                          options = list(placeholder = 'Please select a molecular feature', onInitialize = I('function() { this.setValue(""); }')),
                          selected = "ABCC3"
     )
   })
 
   ## Drugs ----
   updateSelectizeInput(session = session, inputId = 'select_specific_drug',
-                       label = 'Drug Selection:', choices = drugs_search$drugs, server = TRUE,
+                       label = 'Drug selection:', choices = drugs_search$drugs, server = TRUE,
                        options = list(placeholder = 'Please select a drug', onInitialize = I('function() { this.setValue(""); }')),
                        selected = "YM-155"
   )

inst/shinyapp/modules/07_PharmacoGenomics/FeatureAcrossType.R

@@ -19,19 +19,19 @@ uiFeatureAcrossType <- function(id){
       # Select specific feature ----
       column(4,
              selectizeInput(
-               ns("select_specific_feature"), "Features Selection:", choices = NULL,
+               ns("select_specific_feature"), "Feature selection:", choices = NULL,
                options = list(
                  placeholder = 'Please select a feature',
                  onInitialize = I('function() { this.setValue(""); }'), selected = "LAPATINIB"
                ))
              # DOPselectDrugsUI("DOPselectDrugs"),
       ),
       # Select trait to profile ----
-      column(4,
-             selectInput(inputId = ns("select_trait"), 
-                         "Please select the trait type:", 
-                         choices = c("Cell_Type_Source"), selected = "Cell_Type_Source"
-             )),
+      # column(4,
+      #        selectInput(inputId = ns("select_trait"), 
+      #                    "Please select the trait type:", 
+      #                    choices = c("Cell_Type_Source"), selected = "Cell_Type_Source"
+      #        ))
     ),
     # Plot results ----
     wellPanel(
@@ -63,7 +63,7 @@ serverFeatureAcrossType <- function(input, output, session){
                                            "mutation_site" = omics_search[omics_search$type %in% "mutation_site",]$omics,
                                            "fusion" = omics_search[omics_search$type %in% "fusion",]$omics)
     updateSelectizeInput(session = session, inputId = 'select_specific_feature',
-                         label = 'Features Selection:', choices = features_search_sel$features, server = TRUE,
+                         label = 'Feature Selection:', choices = features_search_sel$features, server = TRUE,
                          options = list(placeholder = 'Please select a feature', onInitialize = I('function() { this.setValue(""); }')),
                          selected = "ABCC3"
     )

inst/shinyapp/modules/07_PharmacoGenomics/FeatureDatabaseSig_singlethread.R

@@ -20,7 +20,7 @@ uiFeatureDatabaseSig <- function(id){
       # Select specific feature ----
       column(3,
              selectizeInput(
-               ns("select_specific_feature"), "Features Selection:", choices = NULL,
+               ns("select_specific_feature"), "Feature Selection:", choices = NULL,
                options = list(
                  placeholder = 'Please select a feature',
                  onInitialize = I('function() { this.setValue(""); }'), selected = ""
@@ -87,7 +87,7 @@ serverFeatureDatabaseSig <- function(input, output, session){
                                            "mutation_site" = omics_search[omics_search$type %in% "mutation_site",]$omics,
                                            "fusion" = omics_search[omics_search$type %in% "fusion",]$omics)
     updateSelectizeInput(session = session, inputId = 'select_specific_feature',
-                         label = 'Features Selection:', choices = features_search_sel$features, server = TRUE,
+                         label = 'Feature Selection:', choices = features_search_sel$features, server = TRUE,
                          options = list(placeholder = 'Please select a feature', onInitialize = I('function() { this.setValue(""); }')),
                          selected = ""
     )

inst/shinyapp/modules/07_PharmacoGenomics/ProfileDrugSens.R

@@ -14,20 +14,19 @@ uiProfileDrugSens <- function(id){
       mainPanel(
         column(6,
                radioButtons(inputId = ns("Select_profile_type"), 
-                            strong("Visualization Types"),
+                            strong("Visualization Type:"),
                             choices = list("TSNE" = "TSNE",
                                            "MAD&MEDIAN" = "MAD"), selected = "TSNE")),
         column(6,
                selectizeInput(
-                 ns("select_specific_drug"), "Drugs Selection", choices = NULL,
+                 ns("select_specific_drug"), "Drug Selection:", choices = NULL,
                  options = list(
                    placeholder = 'You can highlight targeted drug',
                    onInitialize = I('function() { this.setValue(""); }'), selected = ""
                  ))
         ),
         column(12,
-               plotly::plotlyOutput(ns("p_drug_sens")),
-               # p("You can interact with the above ggplotly-based plot", align = "center"))
+               plotly::plotlyOutput(ns("p_drug_sens"))
         )
       )
     ))
@@ -47,7 +46,7 @@ serverProfileDrugSens <- function(input, output, session){
                                   "Prism" = drugs_search2[drugs_search2$type %in% "Prism",]$drugs
     )
     updateSelectizeInput(session = session, inputId = 'select_specific_drug',
-                         label = 'Drugs Selection', choices = drugs_search3$drugs, server = TRUE,
+                         label = 'Drug Selection:', choices = drugs_search3$drugs, server = TRUE,
                          options = list(placeholder = 'You can highlight targeted drug', onInitialize = I('function() { this.setValue(""); }')),
                          selected = ""
     )

inst/shinyapp/server/modules.R

@@ -1,3 +1,6 @@
+html_spin = tagList(spin_1(), br(),
+                    h2("Loading independent modules (Only needed for the first time)"))
+
 # # quick module
 observeEvent(req(input$navbar=="TCGA (GTEx): Molecular comparison"),{
   callModule(server.modules_1_tcga_01, "modules_1_tcga_01")
@@ -23,9 +26,9 @@ observeEvent(req(input$navbar=="TCGA: Dimension reduction"),{
   callModule(server.modules_1_tcga_11, "modules_1_tcga_11")
 }, once = TRUE)  
 
-observeEvent(req(input$navbar=="TCGA: Pathway cross analysis"),{
-  callModule(server.modules_1_tcga_12, "modules_1_tcga_12")
-}, once = TRUE)  
+# observeEvent(req(input$navbar=="TCGA: Pathway cross analysis"),{
+#   callModule(server.modules_1_tcga_12, "modules_1_tcga_12")
+# }, once = TRUE)  
 
 observeEvent(req(input$navbar=="PCAWG: Molecular comparison"),{
   callModule(server.modules_2_pcawg_01, "modules_2_pcawg_01")
@@ -50,7 +53,7 @@ observeEvent(req(input$navbar=="CCLE: Molecular correlation"),{
 }, once = TRUE)   
 
 observeEvent(req(input$navbar=="CCLE: Drug analysis"),{
-  waiter <- waiter::Waiter$new(color = "grey", fadeout = TRUE)
+  waiter <- waiter::Waiter$new(color = "grey", fadeout = TRUE, html = html_spin)
   waiter$show()
   callModule(server.modules_3_ccle_03, "modules_3_ccle_03")
   callModule(server.modules_3_ccle_04, "modules_3_ccle_04")
@@ -60,8 +63,7 @@ observeEvent(req(input$navbar=="CCLE: Drug analysis"),{
 
 
 ## TPC 
-html_spin = tagList(spin_1(), br(),
-                    h2("Loading (Only needed for the first time)"))
+
 # TCGA pancan
 observeEvent(req(input$navbar=="TCGA: Correlation Analysis"),{
     waiter <- waiter::Waiter$new(color = "grey", fadeout = TRUE, html = html_spin)
@@ -147,7 +149,7 @@ observeEvent(req(input$navbar=="CCLE: Comparison Analysis"),{
 
 # # identifier help
 observeEvent(req(input$navbar=="TPC ID Query"),{
-  waiter <- waiter::Waiter$new(color = "grey", fadeout = TRUE)
+  waiter <- waiter::Waiter$new(color = "grey", fadeout = TRUE, html = html_spin)
   waiter$show()
 	callModule(server.modules_id_reference, "modules_id_reference")
   on.exit(waiter$hide())
@@ -174,14 +176,14 @@ observeEvent(req(input$navbar=="The Repository Dataset"),{
 
 # PharmacoGenomics
 observeEvent(req(input$navbar %in% c(
-  "Drugs-omics pairs Analysis",
-  "Profiles Display: Features across different types",
-  "Profiles Display: Profile of drug sensitivity",
-  "Features database significant analysis",
+  "Drug-Omics Correlation Analysis",
+  "Feature Abundance Profile in Databases",
+  "Dimension Reduction Profile of Cell Drug Sensitivity",
+  "Feature Scaling Association Analysis",
   "Statistics and Annotations"
 )),{
 
-    waiter <- waiter::Waiter$new(color = "grey", fadeout = TRUE)
+    waiter <- waiter::Waiter$new(color = "grey", fadeout = TRUE, html = html_spin)
     waiter$show()
     message("Preprocessing drug omics data...")
     source(system.file("shinyapp/PGdata.R", package = "UCSCXenaShiny"))

inst/shinyapp/ui/PharmacoGenomics.R

@@ -1,24 +1,24 @@
 ui.page_PharmacoGenomics <- function() {
   navbarMenu(
-    title = "PharmacoGenomics Analysis",
+    title = "PharmacoGenomics",
     icon = icon("buromobelexperte"),
-    ## Drugs-omics pairs analysis ----
+    ## Drug-Omics Correlation Analysis ----
     tabPanel(
-      "Drugs-omics pairs Analysis",
+      "Drug-Omics Correlation Analysis",
       uiDrugOmicPair("DrugOmicPair")
     ),
     ## Profiles Display ----
     tabPanel(
-      "Profiles Display: Features across different types",
+      "Feature Abundance Profile in Databases",
       uiFeatureAcrossType("FeatureAcrossType")
     ),
     tabPanel(
-      "Profiles Display: Profile of drug sensitivity",
+      "Dimension Reduction Profile of Cell Drug Sensitivity",
       uiProfileDrugSens("ProfileDrugSens")  
     ),
     ## Features database significant analysis ----
     tabPanel(
-      "Scaling features associations analysis",
+      "Feature Scaling Association Analysis",
       uiFeatureDatabaseSig("FeatureDatabaseSig")
     ),
     ## Statistics and Annotations ----

inst/shinyapp/ui/home.R

@@ -166,7 +166,7 @@ ui.page_home <- function() {
         column(12, #offset = 1,
           tags$ul(
             tags$li("2024-06-25: Design gene and pathway cross-omics analysis",style = "font-size: 20px;"),
-            tags$li("2024-02-14: Incorporate the PharmacoGenomics analysis modules",style = "font-size: 20px;"),
+            tags$li("2024-02-14: Incorporate the PharmacoGenomics modules",style = "font-size: 20px;"),
             tags$li("2024-01-21: Adjust homepge with slick gallery to show basic page help.",style = "font-size: 20px;"),
             tags$li("2024-01-16: Introduce MSigDB genesets for molecule batch analysis.",style = "font-size: 20px;"),
             tags$li("2023-12-20: Add download modules that support data requisition.",style = "font-size: 20px;"),

inst/shinyapp/ui/link2advanced.R

@@ -9,7 +9,7 @@ ui.link2advanced <- function() {
     # tabPanel(a("Personalized T·P·C Pipelines", 
     #            href="https://lishensuo.github.io/UCSCXenaShiny_Book/",
     #            target="_blank")),
-    # tabPanel(a("PharmacoGenomics Analysis", 
+    # tabPanel(a("PharmacoGenomics", 
     #            href="https://lishensuo.github.io/UCSCXenaShiny_Book/",
     #            target="_blank")),
   )