diff --git a/components/app/R/server.R b/components/app/R/server.R
index cecd5aef5..0f8b9baa1 100644
--- a/components/app/R/server.R
+++ b/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")
}
diff --git a/components/app/R/ui.R b/components/app/R/ui.R
index 59b92d360..c8b3301d7 100644
--- a/components/app/R/ui.R
+++ b/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"),
diff --git a/components/app_idconvert/R/idconvert_server.R b/components/app_idconvert/R/idconvert_server.R
index e87291d4a..4ddb5419d 100644
--- a/components/app_idconvert/R/idconvert_server.R
+++ b/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
})
diff --git a/components/app_idconvert/R/idconvert_ui.R b/components/app_idconvert/R/idconvert_ui.R
index a1464edee..4af475406 100644
--- a/components/app_idconvert/R/idconvert_ui.R
+++ b/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 — annotate your features")
+
+ board <- OmicsBoardUI(
ns = ns,
- title = "ID Converter",
- header_margin="0px",
- board
+ title = title,
+ info = FALSE,
+ header_margin = "0px",
+ ui
)
-
- return(ui)
+
+ return(board)
}
diff --git a/components/app_launcher/R/launcher_ui.R b/components/app_launcher/R/launcher_ui.R
index 1535846f6..c0e441046 100644
--- a/components/app_launcher/R/launcher_ui.R
+++ b/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"
diff --git a/components/app_prism/R/prism_ui.R b/components/app_prism/R/prism_ui.R
index 9227855f5..19bc8e4dc 100644
--- a/components/app_prism/R/prism_ui.R
+++ b/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 — chat and plot")
+
ui <- OmicsBoardUI(
ns = ns,
- title = "SmartPrism",
- header_margin="0px",
+ title = title,
+ header_margin = "0px",
+ info = FALSE,
tags.head,
board
)
diff --git a/components/board.mofa/R/board_mofa_ui.R b/components/board.mofa/R/board_mofa_ui.R
index 2506122d7..fca690597 100644
--- a/components/board.mofa/R/board_mofa_ui.R
+++ b/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,
diff --git a/scss/components/_all.scss b/scss/components/_all.scss
index c5a86e3be..a81592494 100644
--- a/scss/components/_all.scss
+++ b/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 {