modify .opt_pancan (#348)

openbiox · Aug 7, 2024 · 4523aa0 · 4523aa0
1 parent 0a2ba76
commit 4523aa0
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Showing 3 changed files with 16 additions and 6 deletions.
diff --git a/R/query_general.R b/R/query_general.R
@@ -334,9 +334,12 @@ query_general_value <- function(L1, L2, L3,
     }
   } else {
     if (is.null(tpc_value_nonomics)) {
-      tpc_value_nonomics <- load_data(paste0("v2_", database, "_value_nonomics"))
+      if(database=="toil"){
+        tpc_value_nonomics <- load_data(paste0("v2_tcga_value_nonomics"))
+      } else {
+        tpc_value_nonomics <- load_data(paste0("v2_", database, "_value_nonomics"))
+      }
     }
-
     if (L2 != "Custom metadata") {
       L1_label <- switch(L1,
         `Tumor index` = "Index",

diff --git a/R/query_value.R b/R/query_value.R
@@ -60,7 +60,7 @@ query_molecule_value <- function(dataset, molecule, host = NULL) {
   toil_transcript = list(),
   toil_protein = list(),
   toil_mutation = list(),
-  toil_cnv = list(gistic2 = TRUE, use_thresholded_data = FALSE),
+  toil_cnv = list(gistic2 = TRUE, use_thresholded_data = TRUE),
   toil_methylation = list(type = "450K", rule_out = NULL, aggr = "NA"),
   toil_miRNA = list(),
   # PCAWG

diff --git a/inst/shinyapp/ui/link2advanced.R b/inst/shinyapp/ui/link2advanced.R
@@ -3,9 +3,16 @@ ui.link2advanced <- function() {
     title = "Advanced analysis",
     icon = icon("question-circle"),
 
-    tabPanel(a("T·P·C Modules", 
-               href="http://localhost:1498/",
-               target="_blank")),
+    tabPanel(a("Whole Functionalities", 
+               href="https://shiny.zhoulab.ac.cn/UCSCXenaShiny/",
+               target="_blank")),    
+
+    tabPanel("Go to T·P·C Modules", 
+              "To be deployed"),
+    tabPanel("Go to T·P·C Pipelinnes", 
+              "To be deployed"),
+    tabPanel("Go to Pharmcogenomics Modules", 
+              "To be deployed"),
     # tabPanel(a("T·P·C Pipelines", 
     #            href="https://lishensuo.github.io/UCSCXenaShiny_Book/",
     #            target="_blank")),