Quality of usage shinycell updates (#23)

* fix: rework project title in snk rule, remove sketch assay from assays for shinycell

* fix: remove sketch assays if exists

* fix: install sc2 from main not deg branch

* fix: build_shinycell.R fix meta removal function

* fix: comment out meta removal for now

* fix: install shinycell main not DEG_page

* fix: remove silent arg

---------

Co-authored-by: Ryan Routsong <ryan.routsong@nih.gov>

Author: rroutsong

docker/ShinyCell2/Dockerfile

@@ -51,6 +51,6 @@ COPY install_packages.R /opt2/install_packages.R
 RUN cd /opt2 && Rscript /opt2/install_packages.R 
 COPY git_installs.sh /opt2/work/git_installs.sh
 RUN cd /opt2/work; ./git_installs.sh
-RUN Rscript -e 'remotes::install_github("OpenOmics/ShinyCell2@deg_page")'
+RUN Rscript -e 'remotes::install_github("OpenOmics/ShinyCell2")'
 ADD build_shinycell.R /usr/bin/build_shinycell.R
-RUN chmod +x /usr/bin/build_shinycell.R
+RUN chmod +x /usr/bin/build_shinycell.R

docker/ShinyCell2/build_shinycell.R

@@ -4,7 +4,7 @@ prompt_for_install <- function(pkg) {
   response <- tolower(readLines("stdin", n = 1))
   if (response == "y") {
     if (pkg == "ShinyCell2") {
-      remotes::install_github("OpenOmics/ShinyCell2@deg_page", quiet = TRUE)
+      remotes::install_github("OpenOmics/ShinyCell2", quiet = TRUE)
     } else {
       install.packages(pkg, quiet = TRUE)
     }
@@ -112,7 +112,7 @@ parser$add_argument(
 args <- parser$parse_args()
 
 if (args$silent) {
-  options(error = traceback(1))
+  options(error = function() traceback(1))
   options(warn = -1)
 }
 
@@ -214,13 +214,14 @@ if (class(seurat_obj) == "SeuratObject") {
 # ShinyCell2 does NOT support:
 #   - celltype "assays" added by azimuth (prediction.score.celltype.l*)
 #   - HTO
+#   - sketch assays for large datasets
 for (assay in Assays(seurat_obj)) {
   if (startsWith(assay, "prediction.score.celltype.l")) {
     seurat_obj[[assay]] <- NULL
   }
 }
 
-unsupported_assays <- c("HTO")
+unsupported_assays <- c("HTO", "sketch")
 for (assay in unsupported_assays) {
   if (assay %in% names(seurat_obj@assays)) {
     cat(paste0(assay, "unsupported assay removed!", sep = " "))
@@ -235,26 +236,44 @@ if (!is.null(max.levels)) {
   config_params$maxLevels <- max.levels
 }
 
-shinycell_config <- do.call(
-  createConfig,
-  c(seurat_obj, config_params)
-)
-
+# Determine which metadata to include based on remove_metas list
 remove_metas <- c()
 
 if (!is.null(rmmeta)) {
   remove_metas <- c(remove_metas, rmmeta)
 }
 
-for (config_label in shinycell_config$ID) {
+# Add any metadata columns related to unsupported assays to remove_metas
+all_meta_cols <- colnames(seurat_obj@meta.data)
+for (meta_col in all_meta_cols) {
   for (assay in unsupported_assays) {
-    if (grepl(assay, config_label, fixed = TRUE)) {
-      remove_metas <- c(remove_metas, config_label)
+    if (grepl(assay, meta_col, fixed = TRUE)) {
+      remove_metas <- c(remove_metas, meta_col)
     }
   }
 }
 
-shinycell_config <- delMeta(shinycell_config, remove_metas)
+# Remove duplicates from remove_metas
+remove_metas <- unique(remove_metas)
+
+# Create meta.to.include: all metadata columns NOT in remove_metas
+meta_to_include <- setdiff(all_meta_cols, remove_metas)
+
+# Add meta.to.include to config parameters if there are columns to include
+if (length(meta_to_include) > 0) {
+  # config_params$meta.to.del <- remove_metas
+  config_params$meta.to.include <- meta_to_include
+}
+
+shinycell_config <- do.call(
+  createConfig,
+  c(seurat_obj, config_params)
+)
+
+# if (!is.null(length(meta_to_include) > 0)) {
+#   shinycell_config$meta.to.del <- remove_metas
+#   shinycell_config <- delMeta(shinycell_config, remove_metas)
+# }
 
 # Build the Shiny Application,
 # in the default location for

workflow/rules/shinycell2.smk

@@ -3,7 +3,7 @@ from textwrap import dedent
 
 seurat_object       = config['seurat_object']
 run_dir             = config['run_dir']
-project_title       = config['project_title']
+project_title       = config['project_title'].replace("\"", "")
 marker_file         = config['marker_file'] if exists(config['marker_file']) else []
 cluster_labels      = config['cluster_labels']
 rmmeta              = config['rmmeta']
@@ -27,24 +27,23 @@ rule shinycodes:
     container: "docker://rroutsong/shinycell2_builder:latest"
     params:
         rname = "shinycodes",
-        project_title = project_title,
         rmmeta = rmmeta,
         max_levels = max_levels,
         assaytouse = assaytouse,
         outdir = join(run_dir, "wd"),
+        title = f'"{project_title}"',
         defred_flag = f"--defred {defaultreduction} " if defaultreduction else "",
         cluster_flag = f"--cluster_labels {cluster_labels} " if cluster_labels else "",
-        marker_flag = lambda w, input: f"--markers {input.marker_list} " if input.marker_list and exists(input.marker_list) else "",
+        marker_flag = lambda w, input: f"--markers {input.marker_list} " if input.marker_list and exists(input.marker_list) else ""
     shell:
         dedent("""
         build_shinycell.R \\
             -j {input.seurat_object} {params.marker_flag} \\
-            --proj {params.project_title} {params.cluster_flag} \\
+            --proj {params.title} {params.cluster_flag} \\
             --rmmeta {params.rmmeta} {params.defred_flag} \\
             -l {params.max_levels} \\
             -a {params.assaytouse} \\
             -o {params.outdir} \\
-            --silent \\
             --codesonly
         """)
 
@@ -57,24 +56,23 @@ rule shinyfiles:
     container: "docker://rroutsong/shinycell2_builder:latest"
     params:
         rname = "shinyfiles",
-        project_title = project_title,
         rmmeta = rmmeta,
         max_levels = max_levels,
         assaytouse = assaytouse,
         wd = join(run_dir, "wd"),
+        title = f'"{project_title}"',
         defred_flag = f"--defred {defaultreduction} " if defaultreduction else "",
         cluster_flag = f"--cluster_labels {cluster_labels} " if cluster_labels else "",
         marker_flag = lambda w, input: f"--markers {input.marker_list} " if input.marker_list and exists(input.marker_list) else "",
     shell:
         dedent("""
         build_shinycell.R \\
             -j {input.seurat_object} {params.marker_flag} \\
-            --proj {params.project_title} {params.cluster_flag} \\
+            --proj {params.title} {params.cluster_flag} \\
             --rmmeta {params.rmmeta} {params.defred_flag} \\
             -l {params.max_levels} \\
             -a {assaytouse} \\
             -o {params.wd} \\
-            --silent \\
             --filesonly
         """)