Multiwgcna

components/app/R/server.R

@@ -172,7 +172,11 @@ app_server <- function(input, output, session) {
     enable_beta = shiny::reactive(input$enable_beta),
     enable_info = shiny::reactive(input$enable_info)
   )
-
+
+  ## observe and set global User options
+  setUserOption(session,'hello', 'world!')
+  observeEvent(input$llm_model,setUserOption(session,'llm_model', input$llm_model))
+
   ## Do not display "Welcome" tab on the menu
   bigdash.hideMenuItem(session, "welcome-tab")
   shinyjs::runjs("sidebarClose()")
@@ -235,7 +239,7 @@ app_server <- function(input, output, session) {
       bigdash.hideMenuElement(session, "GeneSets")
       bigdash.hideMenuElement(session, "Compare")
       bigdash.hideMenuElement(session, "SystemsBio")
-      bigdash.hideMenuElement(session, "MultiOmics (beta)")
+      bigdash.hideMenuElement(session, "MultiOmics")
     }
     # ###################### I STILL HAVE TO REMOVE THE UI!!!!!!!!!!!!!!!!!!!!!!!!!!!!
     MODULES_TO_REMOVE <- xor(MODULES_LOADED, MODULES_ACTIVE) & MODULES_LOADED
@@ -285,7 +289,7 @@ app_server <- function(input, output, session) {
         lapply(names(MODULE.multiomics$module_menu()), function(x) {
           bigdash.removeTab(session, paste0(x, "-tab"))
         })
-        bigdash.hideMenuElement(session, "MultiOmics (beta)")
+        bigdash.hideMenuElement(session, "MultiOmics")
         loaded$multiomics <- 0
       }
     })
@@ -396,7 +400,7 @@ app_server <- function(input, output, session) {
             info("[SERVER] initializing MultiOmics module")
             mod <- MODULE.multiomics
             insertBigTabUI(mod$module_ui())
-            bigdash.showMenuElement(session, "MultiOmics (beta)")
+            bigdash.showMenuElement(session, "MultiOmics")
             lapply(names(MODULE.multiomics$module_menu()), function(x) {
               bigdash.showTab(session, paste0(x, "-tab"))
             })
@@ -503,22 +507,26 @@ app_server <- function(input, output, session) {
       loaded$compare <- 1
       tab_control()
     }
-    if (input$nav %in% c("drug-tab", "wgcna-tab", "tcga-tab", "cell-tab", "pcsf-tab") && loaded$systems == 0) {
+    if (input$nav %in% c("drug-tab", "wgcna-tab", "tcga-tab", "cell-tab",
+      "pcsf-tab", "consensus-tab", "preservation-tab") && loaded$systems == 0) {
       info("[UI:SERVER] reacted: calling Systems module")
       mod <- MODULE.systems
       insertBigTabUI2(mod$module_ui2(), mod$module_menu())
       mod$module_server(PGX)
       loaded$systems <- 1
       tab_control()
     }
-    if (input$nav %in% c("mofa-tab", "mgsea-tab", "snf-tab", "lasagna-tab", "deepnet-tab") && loaded$multiomics == 0) {
+    if (input$nav %in% c("mofa-tab", "mgsea-tab", "snf-tab", "lasagna-tab",
+      "deepnet-tab", "mwgcna-tab") && loaded$multiomics == 0) {
       info("[UI:SERVER] reacted: calling Multi-Omics module")
       mod <- MODULE.multiomics
       insertBigTabUI2(mod$module_ui2(), mod$module_menu())
       mod$module_server(PGX)
       loaded$multiomics <- 1
       tab_control()
     }
+
+
   })
 
 
@@ -713,12 +721,17 @@ app_server <- function(input, output, session) {
 
     has.libx <- dir.exists(file.path(OPG, "libx"))
 
-    ## Beta features
+    ## Hide beta main tabs
     info("[SERVER] disabling beta features")
     bigdash.toggleTab(session, "tcga-tab", show.beta && has.libx)
+    bigdash.toggleTab(session, "consensus-tab", show.beta)
+    bigdash.toggleTab(session, "preservation-tab", show.beta)
+    bigdash.toggleTab(session, "mwgcna-tab", show.beta)        
+
+    ## hide beta subtabs..
     toggleTab("drug-tabs", "Connectivity map (beta)", show.beta) ## too slow
     toggleTab("pathway-tabs", "Enrichment Map (beta)", show.beta) ## too slow
-
+    
     ## Control tab to only be displayed if there is custom fc + baseline fc
     toggleTab("diffexpr-tabs1", "FC-FC comparison", "custom" %in% colnames(PGX$gx.meta$meta[[1]]$fc) && length(colnames(PGX$gx.meta$meta[[1]]$fc)) > 1)
 
@@ -737,8 +750,8 @@ app_server <- function(input, output, session) {
 
     ## Hide PCSF and WGCNA for metabolomics.
     # WGCNA will be available upon gmt refactoring
-    if (DATATYPEPGX == "metabolomics") {
-      info("[SERVER] disabling WGCNA and PCSF for metabolomics data")
+    if (PGX$datatype == "metabolomics") {
+      info("[SERVER] disabling modules for metabolomics data")
       bigdash.hideTab(session, "cmap-tab")
     }
 
@@ -749,6 +762,7 @@ app_server <- function(input, output, session) {
       bigdash.hideTab(session, "wordcloud-tab")
       bigdash.hideTab(session, "cmap-tab")
     }
+
   }
 
   ## -------------------------------------------------------------

components/app/R/ui.R

@@ -146,9 +146,11 @@ app_ui <- function(x) {
           cell = "Cell profiling",
           pcsf = "PCSF",
           wgcna = "WGCNA",
+          consensus = "Consensus WGCNA",
+          preservation = "Preservation WGCNA",          
           tcga = "TCGA survival (beta)"
         ),
-        "MultiOmics (beta)" = MODULE.multiomics$module_menu()
+        "MultiOmics" = MODULE.multiomics$module_menu()
       )
 
       ## filter disabled modules
@@ -353,6 +355,19 @@ app_ui <- function(x) {
                   "Choose a label type to be displayed in the plots",
                   placement = "right", options = list(container = "body")
                 )
+              ),
+              bigdash::navbarDropdownItem(
+                withTooltip(
+                  shiny::selectInput(
+                    inputId = "llm_model",
+                    label = "LLM model:",
+                    choices = c("granite4:micro", "llama3.2:1b", "gpt-5-nano"),
+                    selected = "granite4:micro",
+                    width = "100%"
+                  ),
+                  "Choose a label type to be displayed in the plots",
+                  placement = "right", options = list(container = "body")
+                )
               )
             )
           ),
@@ -373,9 +388,9 @@ app_ui <- function(x) {
             "welcome-tab",
             "BigOmics Playground",
             "is your self-service bioinformatics platform for interactive analysis,
-                    visualization and interpretation of transcriptomics and proteomics data.
-                    Perform complex data analysis and visualization easily without coding,
-                    and significantly reduce the time-to-discovery."
+             visualization and interpretation of transcriptomics and proteomics data.
+             Perform complex data analysis and visualization easily without coding,
+             and significantly reduce the time-to-discovery."
           ),
           bigdash::sidebarTabHelp(
             "load-tab",
@@ -517,6 +532,16 @@ app_ui <- function(x) {
             tspan("Visualize the distribution of (inferred)
                     immune cell types, expressed genes and pathway activation.")
           ),
+          bigdash::sidebarTabHelp(
+            "consensus-tab",
+            "Consensus WGCNA",
+            tspan("Consensus analysis using the WGCNA framework")
+          ),
+          bigdash::sidebarTabHelp(
+            "preservation-tab",
+            "Preservation WGCNA",
+            tspan("Preservation analysis using the WGCNA framework")
+          ),
           !!!MODULE.multiomics$module_help() ### HELP!!! DOES NOT WORK!!!
         ),
         bigdash::bigTabs(

components/app/R/utils/utils.R

@@ -9,6 +9,14 @@
 ##                                                                     ##
 #########################################################################
 
+setUserOption <- function(session, var, value) {
+  session$userData[[var]] <- value
+}
+
+getUserOption <- function(session, var, value) {
+  return(session$userData[[var]])
+}
+
 is.symlink <- function(paths) isTRUE(nzchar(Sys.readlink(paths), keepNA = TRUE))
 
 getAppVersion <- function(add.auth = FALSE) {

components/board.mofa/R/__init.R

@@ -6,9 +6,10 @@ MODULE.multiomics <- list(
     c(
       snf = "SNF",
       lasagna = "LASAGNA",
-      mgsea = "multiGSEA",
+      mgsea = "Multiomics GSEA",
       mofa = "MOFA",
-      deepnet = "DeepLearning"
+      deepnet = "DeepLearning",
+      mwgcna = "Multiomics WGCNA"
     )
   },
   module_ui = function() {
@@ -17,7 +18,8 @@ MODULE.multiomics <- list(
       bigdash::bigTabItem("mgsea-tab", MGseaInputs("mgsea"), create_loader("mgsea-loader")),
       bigdash::bigTabItem("snf-tab", SNFInputs("snf"), create_loader("snf-loader")),
       bigdash::bigTabItem("lasagna-tab", LasagnaInputs("lasagna"), create_loader("lasagna-loader")),
-      bigdash::bigTabItem("deepnet-tab", DeepNetInputs("deepnet"), create_loader("deepnet-loader"))
+      bigdash::bigTabItem("deepnet-tab", DeepNetInputs("deepnet"), create_loader("deepnet-loader")),
+      bigdash::bigTabItem("mwgcna-tab", MultiWGCNA_Inputs("mwgcna"), create_loader("mwgcna-loader"))
     )
   },
   module_ui2 = function() {
@@ -26,7 +28,8 @@ MODULE.multiomics <- list(
       list("mgsea-tab", MGseaUI("mgsea")),
       list("snf-tab", SNFUI("snf")),
       list("lasagna-tab", LasagnaUI("lasagna")),
-      list("deepnet-tab", DeepNetUI("deepnet"))
+      list("deepnet-tab", DeepNetUI("deepnet")),
+      list("mwgcna-tab", MultiWGCNA_UI("mwgcna"))
     )
   },
   module_server = function(PGX) {
@@ -44,30 +47,33 @@ MODULE.multiomics <- list(
 
     info("[SERVER] calling DeepNetBoard module")
     DeepNetBoard("deepnet", pgx = PGX)
+
+    info("[SERVER] calling MultiWGCNABoard module")
+    MultiWGCNA_Board("mwgcna", pgx = PGX)
+
   },
   module_help = function() {
     list(
       bigdash::sidebarTabHelp(
         "mofa-tab", "MOFA",
         tspan("Multi-omics Factor Analysis (MOFA) is a multi-omics
-                  integration method based on matrix factorization.")
-      ),
-      bigdash::sidebarTabHelp(
-        "mgsea-tab", "multiGSEA",
-        tspan("multiGSEA performs multi-omics integration on gene set level.")
-      ),
-      bigdash::sidebarTabHelp(
-        "snf-tab", "SNF",
-        tspan("SNF clustering")
-      ),
-      bigdash::sidebarTabHelp(
-        "lasagna-tab", "Lasagna",
-        tspan("LASAGNA is a stacked layer model for multi-omics integration where each layer corresponds to a datatype.")
-      ),
-      bigdash::sidebarTabHelp(
-        "deepnet-tab", "DeepLearning",
-        tspan("Integration using DeepLearning")
-      )
+                  integration method based on matrix factorization.")),
+
+      bigdash::sidebarTabHelp("mgsea-tab", "multiGSEA",
+        tspan("multiGSEA performs multi-omics integration on gene set level.")),
+
+      bigdash::sidebarTabHelp("snf-tab", "SNF",
+        tspan("SNF clustering")),
+
+      bigdash::sidebarTabHelp("lasagna-tab", "Lasagna",
+        tspan("LASAGNA is a stacked layer model for multi-omics integration where each layer corresponds to a datatype.")),
+
+      bigdash::sidebarTabHelp("deepnet-tab", "DeepLearning",
+        tspan("Integration using DeepLearning")),
+
+      bigdash::sidebarTabHelp("mwgcna-tab", "MultiOmics WGCNA",
+        tspan("WGCNA for multi-omics"))
+
     )
   }
 )

components/board.mofa/R/board_lasagna_server.R

@@ -197,7 +197,7 @@ LasagnaBoard <- function(id, pgx) {
         gsfilter <- list(gset = input$gsfilter)
       }
 
-      edge.sign <- ifelse(input$pos_edges, "pos", "both")
+      edge.sign <- ifelse(input$consensus, "consensus", "both")
 
       ## prune graph for plotting
       pruned <- playbase::lasagna.prune_graph(

components/board.mofa/R/board_lasagna_ui.R

@@ -37,10 +37,10 @@ LasagnaInputs <- function(id) {
         "Network options",
         icon = icon("cog", lib = "glyphicon"),
         shiny::tagList(
-          ## shiny::checkboxInput(ns("top50"),"top 50",TRUE),
-          shiny::checkboxInput(ns("pos_edges"), "positive edges", FALSE),
-          shiny::checkboxInput(ns("sp_weight"), "SP weighting", FALSE),
-          shiny::sliderInput(ns("minrho"), "Edge threshold:", 0, 0.95, 0.5, 0.05),
+          ##shiny::checkboxInput(ns("top50"),"top 50",TRUE),
+          shiny::checkboxInput(ns("consensus"),"consensus",FALSE),          
+          shiny::checkboxInput(ns("sp_weight"),"SP weighting",FALSE),
+          shiny::sliderInput(ns("minrho"),"Edge threshold:",0,0.95,0.5,0.05),
           shiny::hr(),
           shiny::radioButtons(ns("node_value"), "Node value:",
             choices = c("logFC", "rho"), selected = "logFC", inline = TRUE

components/board.wgcna/R/__init.R

@@ -10,7 +10,9 @@ MODULE.systems <- list(
       wgcna = "Network analysis",
       tcga = "TCGA analysis",
       cell = "Single cell",
-      pcsf = "Protein networks"
+      pcsf = "Protein networks",
+      consensus = "Consensus WGCNA",
+      preservation = "Preservation WGCNA"
     )
   },
   module_ui = function() {
@@ -39,6 +41,16 @@ MODULE.systems <- list(
         "pcsf-tab",
         PcsfInputs("pcsf"),
         create_loader("pcsf-loader")
+      ),
+      bigdash::bigTabItem(
+        "consensus-tab",
+        ConsensusWGCNA_Inputs("consensus"),
+        create_loader("consensus-loader")
+      ),
+      bigdash::bigTabItem(
+        "preservation-tab",
+        PreservationWGCNA_Inputs("preservation"),
+        create_loader("preservation-loader")
       )
     )
   },
@@ -63,6 +75,14 @@ MODULE.systems <- list(
       list(
         "pcsf-tab",
         PcsfUI("pcsf")
+      ),
+      list(
+        "consensus-tab",
+        ConsensusWGCNA_UI("consensus")
+      ),
+      list(
+        "preservation-tab",
+        PreservationWGCNA_UI("preservation")
       )
     )
   },
@@ -86,5 +106,16 @@ MODULE.systems <- list(
     PcsfBoard("pcsf",
       pgx = PGX
     )
+
+    ConsensusWGCNA_Board(
+      id = "consensus",
+      pgx = PGX
+    )     
+
+    PreservationWGCNA_Board(
+      id = "preservation",
+      pgx = PGX
+    )     
+
   }
 )