feat: enable mini apps (devmode only)

components/app/R/server.R

@@ -755,7 +755,7 @@ output$current_user <- shiny::renderText({
     raw_dir <- shiny::isolate(raw_dir())
 
     if (!is.null(PGX) && !is.null(shiny::isolate(PGX$name))) {
-      pgx_name <- PGX$name
+      pgx_name <- shiny::isolate(PGX$name)
     } else {
       pgx_name <- "No PGX loaded when error occurred"
     }
@@ -1065,13 +1065,12 @@ output$current_user <- shiny::renderText({
   }
 
   launch_prism <- function() {
-    launchModule("Prism",
+    launchModule("prism",
       ui = omicspanel(prism_ui("prism")),
       server = function() prism_server("prism")
     )
   }
-
-  ## THESE STILL NEED TO BE WRAPPED in a launchModule()
+
   if(isTRUE(opt$DEVMODE)) {
     RunMonitorServer("runmonitor")
   }

components/app/R/ui.R

@@ -181,23 +181,6 @@ app_ui <- function(x) {
                 omicspanel(AdminPanelUI("admin_panel"))
               )
             },
-            ## Tools
-            ## if(isTRUE(opt$DEVMODE)) {
-            ##   bslib::nav_panel_hidden("Prism",
-            ##     omicspanel(prism_ui("prism"))
-            ##   )
-            ## },
-            ## if(isTRUE(opt$DEVMODE)) {
-            ##   bslib::nav_panel_hidden("IDconvert",
-            ##     omicspanel(idconvert_ui("idconvert"))
-            ##   )
-            ## },
-            ## if(isTRUE(opt$DEVMODE)) {
-            ##   bslib::nav_panel_hidden(
-            ##     value = "AcrossDatasets",
-            ##     omicspanel(AcrossUI("across"))
-            ##   )
-            ## },
             ## lower settings buttons
             bslib::nav_spacer(),
             bslib::nav_panel("Settings", icon=icon("cog"),

components/app_idconvert/R/idconvert_server.R

@@ -47,7 +47,7 @@ convert_datatype_choices <- function() {
 idconvert_server <- function(id) {
   shiny::moduleServer(id, function(input, output, session) {
 
-    supported_organisms <- convert_organism_choices()    
+    supported_organisms <- convert_organism_choices()
     shiny::updateSelectizeInput(session, "organism",
       choices = supported_organisms, selected = "Human", server = TRUE
     )
@@ -119,7 +119,7 @@ idconvert_server <- function(id) {
         !is.null(annot),
         "Could not annotate these IDs for the selected organism."
       ))
-
+      
       result(annot)  # store successful result
     })
 

components/app_idconvert/R/idconvert_ui.R

@@ -7,22 +7,25 @@ idconvert_ui <- function(id) {
   ns <- shiny::NS(id) ## namespace
 
   organism_choices <- convert_organism_choices()
-  
-  board <- bslib::layout_columns(
+
+  ui <- bslib::layout_columns(
     col_widths = c(2, 10),
+    class = "p-3",
+    gap = "0.7rem",
+    height = "100%",
+    row_heights = "auto",
     bslib::layout_columns(
       col_widths = 12,
+      gap = "14px",
       fill = FALSE,
-      gap = "0.7rem",
-      row_heights = "auto",
-      shiny::selectizeInput(
-        ns("organism"), "Organism:",
-        choices = NULL,
+      shiny::selectizeInput(ns("organism"), "Organism:",
+        choices = c("Human" = "Human"),
+        selected = "Human",
         options = list(maxOptions = length(organism_choices))
       ),
       shiny::div(
         paste(length(organism_choices), "species available"),
-        style = "font-size: 11px; color: #888; margin: -8px 0 0 0;"
+        style = "font-size: 12px; color: #888; margin: -12px 0 0 0;"
       ),
       shiny::selectInput(ns("datatype"), "Datatype:",
         choices = convert_datatype_choices(),
@@ -70,12 +73,15 @@ idconvert_ui <- function(id) {
     )
   )
 
-  ui <- OmicsBoardUI(
+  title <- HTML("ID Annotator <span style='font-size: 0.7em;'>&mdash; annotate your features</span>")
+
+  board <- OmicsBoardUI(
     ns = ns,
-    title = "ID Converter",
-    header_margin="0px",
-    board
+    title = title,
+    info = FALSE,
+    header_margin = "0px",
+    ui
   )
-
-  return(ui)
+  
+  return(board)
 }

components/app_launcher/R/launcher_ui.R

@@ -62,7 +62,7 @@ launcher_ui <- function(id) {
     list(
       input = "launch_idconvert",
       icon = "shuffle",
-      label = "ID Converter",
+      label = "ID Annotator",
       description = "Annotate features",
       rgb = c(140,35,175),
       group = "Apps",
@@ -72,7 +72,7 @@ launcher_ui <- function(id) {
       input = "launch_prism",
       icon = "wand-magic-sparkles",
       label = "SmartPrism",
-      description = "AI-generated figures",
+      description = "AI-assisted plotting",
       rgb = c(190,120,50),
       group = "Apps",
       badge = "dev"

components/app_prism/R/prism_ui.R

@@ -17,8 +17,6 @@ prism_ui <- function(id) {
       actionButton(ns("button4"), "button4", icon=icon("eye-dropper"))
     )
   )
-
-  title <- div("SmartPrism", style="font-size: 18px;")
 
   tags.head <- tags$head(
     tags$script(type = "module", src = "static/prism-webr.js"),
@@ -123,10 +121,13 @@ prism_ui <- function(id) {
     )        
   )
 
+  title <- HTML("SmartPrism <span style='font-size: 0.7em;'>&mdash; chat and plot</span>")
+
   ui <- OmicsBoardUI(
     ns = ns,
-    title = "SmartPrism",
-    header_margin="0px",
+    title = title,
+    header_margin = "0px",
+    info = FALSE,
     tags.head,
     board
   )

components/board.mofa/R/board_mofa_ui.R

@@ -275,6 +275,7 @@ MofaUI <- function(id) {
 
   #  shiny::div(
   bslib::page_fillable(
+    padding = 0,
     fillable_mobile = FALSE, # not working here...
     OmicsBoardUI(
       ns = ns,

scss/components/_all.scss

@@ -353,12 +353,13 @@ html {
   }
 
   div#navheader-current-section {
+    height: 33px;
     font-size: 28px;
     font-weight: 600;
     // 17px tighter than it used to be (was margin-top 15 + padding-top 10):
     // this puts the title's baseline on the same line as the sidebar's "Menu"
     // heading instead of floating well below it.
-    margin: 8px 0 5px 0px;
+    margin: 8px 0 5px 15px;
   }
 
   div#navheader-dataset-stats {