Multiple fixes:

- Fix: loading of light_version bundles was broken.
- Fix: `projection_point_size` and `scatters_point_size` were not detected when added in `other_params`.
- Fix: import warned when there were metacells withour an edge when providing `default_graph` parameter.

* `About` tab is now the first in light-version bundles.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MCView
 Title: A Shiny App for Metacell Analysis
-Version: 0.2.25
+Version: 0.2.26
 Authors@R: 
     person(given = "Aviezer",
            family = "Lifshitz",

NEWS.md

@@ -1,3 +1,12 @@
+# MCView 0.2.6 
+
+* Multiple fixes:
+- Fix: loading of light_version bundles was broken.
+- Fix: `projection_point_size` and `scatters_point_size` were not detected when added in `other_params`. 
+- Fix: import warned when there were metacells withour an edge when providing `default_graph` parameter.
+
+* `About` tab is now the first in light-version bundles. 
+
 # MCView 0.2.5 
 
 * Added an option to exclude lateral and noisy genes from marker heatmap.

R/app_config.R

@@ -212,6 +212,13 @@ init_tab_defs <- function() {
 
     cur_config$tabs <- order_tabs(cur_config$tabs)
 
+    if (!is.null(config$light_version) && config$light_version) {
+        # make the About tab first if exists
+        if ("About" %in% cur_config$tabs) {
+            cur_config$tabs <- c("About", cur_config$tabs[cur_config$tabs != "About"])
+        }
+    }
+
     config <<- cur_config
 }
 

R/plot_gene_mc.R

@@ -153,6 +153,8 @@ connect_gene_plots <- function(input, output, session, ns, source) {
 initial_scatters_point_size <- function(dataset, screen_width = NULL, screen_height = NULL, weight = 1, atlas = FALSE) {
     if (!is.null(config$datasets[[dataset]]$scatters_point_size)) {
         return(config$datasets[[dataset]]$scatters_point_size)
+    } else if (!is.null(config$scatters_point_size)) {
+        return(config$scatters_point_size)
     }
     n_metacells <- length(get_mc_data(dataset, "mc_sum", atlas = atlas))
     screen_width <- screen_width %||% 1920
@@ -166,6 +168,8 @@ initial_scatters_point_size <- function(dataset, screen_width = NULL, screen_hei
 initial_scatters_stroke <- function(dataset) {
     if (!is.null(config$datasets[[dataset]]$scatters_stroke)) {
         return(config$datasets[[dataset]]$scatters_stroke)
+    } else if (!is.null(config$scatters_stroke)) {
+        return(config$scatters_stroke)
     }
     return(0.2)
 }

R/plot_mc2d_proj.R

@@ -433,6 +433,8 @@ render_2d_plotly <- function(input, output, session, dataset, metacell_types, ce
 initial_proj_point_size <- function(dataset, screen_width = NULL, screen_height = NULL, weight = 1, atlas = FALSE) {
     if (!is.null(config$datasets[[dataset]]$projection_point_size)) {
         return(config$datasets[[dataset]]$projection_point_size * weight)
+    } else if (!is.null(config$projection_point_size)) {
+        return(config$projection_point_size * weight)
     }
     n_metacells <- length(get_mc_data(dataset, "mc_sum", atlas = atlas))
     screen_width <- screen_width %||% 1920

R/umap.R

@@ -174,10 +174,10 @@ layout_and_graph_to_mc2d <- function(layout, graph, metacells, warn_function = c
         return(NULL)
     }
 
-    unknown_metacells <- c(setdiff(metacells, graph$from), setdiff(metacells, graph$to))
+    unknown_metacells <- c(setdiff(graph$from, metacells), setdiff(graph$to, metacells))
     if (length(unknown_metacells) > 0) {
         unknown_metacells <- paste(unknown_metacells, collapse = ", ")
-        warn_function(glue("Metacells {unknown_metacells} were not found in layout"))
+        warn_function(glue("Metacells {unknown_metacells} were in the graph but not in the dataset"))
     }
 
     graph <- graph %>% filter(from %in% metacells, to %in% metacells)

R/utils_heatmap.R

@@ -68,6 +68,8 @@ heatmap_sidebar <- function(id, ...) {
         add_genes_ui <- NULL
         update_genes_ui <- NULL
         load_genes_ui <- NULL
+        include_lateral_ui <- NULL
+        include_noisy_ui <- NULL
     } else {
         max_gene_num_ui <- numericInput(ns("max_gene_num"), "Maximal number of genes", value = 100)
         remove_genes_ui <- shinyWidgets::actionGroupButtons(ns("remove_genes"), labels = "Remove selected genes", size = "sm")

R/utils_selectors.R

@@ -85,11 +85,13 @@ metadata_selector <- function(dataset, ns, id = "selected_md", label = "Metadata
         metadata <- get_mc_data(dataset(), metadata_id)
         req(metadata)
         metadata_fields <- c(additional_fields, colnames(metadata)[-1])
-        shinyWidgets::pickerInput(ns(id), label,
+        shinyWidgets::virtualSelectInput(ns(id),
+            label = label,
             choices = metadata_fields,
             selected = selected,
             multiple = multiple,
-            options = list(`actions-box` = TRUE, `dropup-auto` = FALSE)
+            showSelectedOptionsFirst = TRUE,
+            search = TRUE
         )
     })
 }