biopipen 0.34.12__tar.gz → 0.34.14__tar.gz

{biopipen-0.34.12 → biopipen-0.34.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biopipen
-Version: 0.34.12
+Version: 0.34.14
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.34.14/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.34.14"

{biopipen-0.34.12 → biopipen-0.34.14}/biopipen/ns/scrna.py

@@ -1097,8 +1097,6 @@ class MarkersFinder(Proc):
                 - res (type=int): The resolution of the plots.
                 - height (type=int): The height of the plots.
                 - width (type=int): The width of the plots.
-            - order_by: an expression to order the markers, passed by `dplyr::arrange()`.
-            - genes: The number of top genes to show or an expression passed to `dplyr::filter()` to filter the genes.
             - <more>: Other arguments passed to [`biopipen.utils::VizDEGs()`](https://pwwang.github.io/biopipen.utils.R/reference/VizDEGs.html).
         allmarker_plots (type=json): All marker plot cases.
             The keys are the names of the cases and the values are the dicts inherited from `allmarker_plots_defaults`.
@@ -1123,8 +1121,6 @@ class MarkersFinder(Proc):
                 - res (type=int): The resolution of the plots.
                 - height (type=int): The height of the plots.
                 - width (type=int): The width of the plots.
-            - order_by: an expression to order the markers, passed by `dplyr::arrange()`.
-            - genes: The number of top genes to show or an expression passed to `dplyr::filter()` to filter the genes.
             - <more>: Other arguments passed to [`biopipen.utils::VizDEGs()`](https://pwwang.github.io/biopipen.utils.R/reference/VizDEGs.html).
                 If `plot_type` is `volcano_pct` or `volcano_log2fc`, they will be passed to
                 [`scplotter::VolcanoPlot()`](https://pwwang.github.io/plotthis/reference/VolcanoPlot.html).
@@ -1196,8 +1192,6 @@ class MarkersFinder(Proc):
             "more_formats": [],
             "save_code": False,
             "devpars": {"res": 100},
-            "order_by": "desc(abs(avg_log2FC))",
-            "genes": 10,
         },
         "allmarker_plots": {},
         "allenrich_plots_defaults": {
@@ -1210,8 +1204,6 @@ class MarkersFinder(Proc):
             "more_formats": [],
             "save_code": False,
             "devpars": {"res": 100},
-            "order_by": "desc(abs(avg_log2FC))",
-            "genes": 10,
         },
         "marker_plots": {
             "Volcano Plot (diff_pct)": {"plot_type": "volcano_pct"},

{biopipen-0.34.12 → biopipen-0.34.14}/biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R

@@ -111,7 +111,8 @@ if (file.exists(celltypist_outfile) &&
         command <- paste(command, "-v")
     }
     log$info("Running celltypist:")
-    print("- {command}")
+    # print("- {command}")
+    log$debug("  {command}")
     rc <- system(command)
     if (rc != 0) {
         stop("Failed to run celltypist. Check the job.stderr file to see the error message.")

{biopipen-0.34.12 → biopipen-0.34.14}/biopipen/scripts/scrna/MarkersFinder.R

@@ -271,8 +271,9 @@ process_markers <- function(markers, info, case) {
     if (nrow(markers) > 0) {
         for (plotname in names(case$marker_plots)) {
             plotargs <- case$marker_plots[[plotname]]
-            plotargs$degs <- markers
-            rownames(plotargs$degs) <- make.unique(markers$gene)
+            plotargs$markers <- markers
+            plotargs$object <- case$object
+            plotargs$comparison_by <- case$group_by
             plotargs$outprefix <- file.path(info$prefix, paste0("markers.", slugify(plotname)))
             do_call(VizDEGs, plotargs)
             reporter$add2(
@@ -401,18 +402,18 @@ process_markers <- function(markers, info, case) {
     }
 }
 
-process_allmarkers <- function(markers, plotcases, casename, groupname) {
+process_allmarkers <- function(markers, object, comparison_by, plotcases, casename, groupname, subset_by_group = TRUE) {
     name <- paste0(casename, "::", paste0(groupname, " (All Markers)"))
     info <- case_info(name, outdir, create = TRUE)
 
     for (plotname in names(plotcases)) {
         plotargs <- plotcases[[plotname]]
-        plotargs$degs <- markers
+        plotargs$markers <- markers
+        plotargs$object <- object
+        plotargs$comparison_by <- comparison_by
+        if (subset_by_group)
+            plotargs$subset_by <- groupname
         plotargs$outprefix <- file.path(info$prefix, slugify(plotname))
-        if (identical(plotargs$plot_type, "heatmap")) {
-            plotargs$show_row_names = plotargs$show_row_names %||% TRUE
-            plotargs$show_column_names = plotargs$show_column_names %||% TRUE
-        }
         do_call(VizDEGs, plotargs)
         reporter$add2(
             list(
@@ -529,6 +530,7 @@ run_case <- function(name) {
         case,
         "dbs", "sigmarkers", "allmarker_plots", "allenrich_plots", "marker_plots", "enrich_plots",
         "overlaps", "original_case", "markers", "enriches", "each_name", "each", "enrich_style", "original_subset",
+        subset_ = "subset",
         allow_nonexisting = TRUE
     )
 
@@ -562,7 +564,14 @@ run_case <- function(name) {
                 attr(markers, "ident_1") <- NULL
                 attr(markers, "ident_2") <- NULL
                 if (!is.null(markers) && nrow(markers) > 0) {
-                    process_allmarkers(markers, allmarker_plots, name, each)
+                    process_allmarkers(
+                        markers,
+                        object = if (is.null(original_subset)) srtobj else filter(srtobj, !!parse_expr(original_subset)),
+                        comparison_by = group_by,
+                        allmarker_plots,
+                        name,
+                        each
+                    )
                 }
             }
 
@@ -598,11 +607,15 @@ run_case <- function(name) {
         return(invisible())
     }
 
+    # Let RunSeuratDEAnalysis handle the subset
+    case$subset <- subset_
     case$object <- srtobj
     markers <- do_call(RunSeuratDEAnalysis, case)
-    case$object <- NULL
+    case$object <- NULL  # Release memory
     gc()
 
+    subobj <- if (is.null(subset_)) srtobj else filter(srtobj, !!parse_expr(subset_))
+
     if (is.null(case$ident_1)) {
         all_idents <- unique(as.character(markers[[case$group_by]]))
         enriches <- list()
@@ -614,7 +627,9 @@ run_case <- function(name) {
 
             attr(ident_markers, "ident_1") <- ident
             enrich <- process_markers(ident_markers, info = info, case = list(
+                object = subobj,
                 dbs = dbs,
+                group_by = case$group_by,
                 sigmarkers = sigmarkers,
                 enrich_style = enrich_style,
                 marker_plots = marker_plots,
@@ -627,7 +642,14 @@ run_case <- function(name) {
 
         if (length(allmarker_plots) > 0) {
             log$info("- Visualizing all markers together ...")
-            process_allmarkers(markers, allmarker_plots, name, case$group_by)
+            process_allmarkers(
+                markers,
+                object = subobj,
+                comparison_by = case$group_by,
+                plotcases = allmarker_plots,
+                casename = name,
+                groupname = case$group_by,
+                subset_by_group = FALSE)
         }
 
         if (length(overlaps) > 0) {
@@ -642,7 +664,9 @@ run_case <- function(name) {
     } else {
         info <- case_info(name, outdir, create = TRUE)
         enrich <- process_markers(markers, info = info, case = list(
+            object = subobj,
             dbs = dbs,
+            group_by = case$group_by,
             sigmarkers = sigmarkers,
             enrich_style = enrich_style,
             marker_plots = marker_plots,

{biopipen-0.34.12 → biopipen-0.34.14}/biopipen/scripts/scrna/SeuratClusterStats-features.R

@@ -107,7 +107,12 @@ do_one_features <- function(name) {
         caching$restore()
     } else {
         case$features <- .get_features(features, case$object)
-        p <- do_call(gglogger::register(FeatureStatPlot), case)
+        p <- tryCatch({
+            do_call(gglogger::register(FeatureStatPlot), case)
+        }, error = function(e) {
+            if (save_code) { stop(e) }
+            do_call(FeatureStatPlot, case)
+        })
         save_plot(p, info$prefix, devpars, formats = c("png", more_formats))
         if (save_code) {
             save_plotcode(p, info$prefix,

{biopipen-0.34.12 → biopipen-0.34.14}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.34.12"
+version = "0.34.14"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.34.12 → biopipen-0.34.14}/setup.py

@@ -86,7 +86,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.34.12',
+    'version': '0.34.14',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.34.12/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.34.12"