biopipen 0.34.12__py3-none-any.whl → 0.34.14__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.34.12"
+__version__ = "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/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/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/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.dist-info → biopipen-0.34.14.dist-info}/METADATA

@@ -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-0.34.12.dist-info → biopipen-0.34.14.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=HrphpHL7XwXAzTz1RdzYzTTXdA0Tl5ZtQnsmI6sI8bo,24
+biopipen/__init__.py,sha256=EumHAzPCe3UipaK_9iqfQf47_8LP5jWSnXBVUZmzQTA,24
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=lZV_vbYWk6uqm19ZWJcsZCcSNqAdIfN2fOfamzxZpg4,2148
@@ -22,7 +22,7 @@ biopipen/ns/plot.py,sha256=N41_izb6zi-XArUly5WhLebapNXbTNSgGlOCCwtrDlY,18282
 biopipen/ns/protein.py,sha256=YJtlKoHI2p5yHdxKeQnNtm5QrbxDGOq1UXOdt_7tlTs,6391
 biopipen/ns/regulatory.py,sha256=WlnX_R8jEFyxCjk8mru5Qu5iCQJLzjMWiWGoc3gygzc,16221
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=i3LNPJtr3qZeweMnp7Z4x31oRYwkp6KsQrst4epOWEU,146288
+biopipen/ns/scrna.py,sha256=yWG6oQ1XXzhr-GYOouiC_4aEwmi7XS8RW265XWsoqhw,145722
 biopipen/ns/scrna_metabolic_landscape.py,sha256=EwLMrsj_pTqvyAgtHLoishjQxCg_j8n5OofuTofUph0,22096
 biopipen/ns/snp.py,sha256=iXWrw7Lmhf4_ct57HGT7JGTClCXUD4sZ2FzOgsC2pTg,28123
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
@@ -142,7 +142,7 @@ biopipen/scripts/scrna/AnnData2Seurat.R,sha256=wc5PDbK9TkuJtoXXxF4W1ODylWhyfKWd3
 biopipen/scripts/scrna/CCPlotR-patch.R,sha256=KpB8fwacBaWaUNjIidcLUkMShLjS4Gq9UY8LUgIITB0,8369
 biopipen/scripts/scrna/CellCellCommunication.py,sha256=LnEuV8YHOJSYM7Tb_jwLbTQdMSpJw5ChRIiLktcJzSQ,4471
 biopipen/scripts/scrna/CellCellCommunicationPlots.R,sha256=IcqqhVWasSE54PDWaw85u5_yup_YHVNNwZI7oOy9250,2456
-biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=CwYR8WWQMf8r7V2CTalG4kxdKnYMtyhpJBe9zP2sQWA,6964
+biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=FqxVHFNUC7tcOeA5I_IcxzxU0WDLKZrKObgq2PwaVS8,6995
 biopipen/scripts/scrna/CellTypeAnnotation-direct.R,sha256=jwjSBql66ku11b4O_7bIs9zuwbqHiGgrAFDk1tSbwg4,3111
 biopipen/scripts/scrna/CellTypeAnnotation-hitype.R,sha256=vvjhxin4aoA9heecey0dpr6ofirybygY3ApjgtQW89Y,2094
 biopipen/scripts/scrna/CellTypeAnnotation-sccatch.R,sha256=xxB4K1MzBSNQnDxa44s5ExeU67MbncOBf8lGFr7RvwQ,1870
@@ -155,7 +155,7 @@ biopipen/scripts/scrna/ExprImputation-rmagic.R,sha256=ePgbMZ_3bKbeUrjsMdkdtBM_MS
 biopipen/scripts/scrna/ExprImputation-scimpute.R,sha256=MI_bYfvCDKJsuGntUxfx_-NdrssBoQgL95-DGwJVE5s,1191
 biopipen/scripts/scrna/ExprImputation.R,sha256=GcdZJpkDpq88hRQjtLZY5-byp8V43stEFm5T-pQbU6A,319
 biopipen/scripts/scrna/LoomTo10X.R,sha256=c6F0p1udsL5UOlb84-53K5BsjSDWkdFyYTt5NQmlIec,1059
-biopipen/scripts/scrna/MarkersFinder.R,sha256=qBVdxO8cKTJMtGyJLl2QGRrtdiXOJSLXu6rpZUPkDZk,25437
+biopipen/scripts/scrna/MarkersFinder.R,sha256=nz18T_70ni9sfoFYp8weQMCiojphF61l5yHe9f_gOSM,26320
 biopipen/scripts/scrna/MetaMarkers.R,sha256=BgYaWYEj6obwqaZaDWqNPtxb1IEEAnXAeBE0Ji9PvBA,12426
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=_mvo35a-wk5miUb_kMIVwvKK0b6InRa1NKtN8zznGwk,4457
 biopipen/scripts/scrna/PseudoBulkDEG.R,sha256=IuM4hl-KHZ5aaaTqZeylw4b1ZenMZaY4qobD5qxAlHs,25199
@@ -167,7 +167,7 @@ biopipen/scripts/scrna/ScVelo.py,sha256=SPUZFgZW1Zhw-bnjJo98RK0vpuNFODQ8Q3eTguNc
 biopipen/scripts/scrna/Seurat2AnnData.R,sha256=F8g5n2CqX4-KBggxd8ittz8TejYuqqNLMudAHdFt1QM,184
 biopipen/scripts/scrna/SeuratClusterStats-clustree.R,sha256=K2pRNe3qFjTJY3VL4EQFxoU1Lzp5DUavhcfx6HZk2J8,3954
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=2YNUxPz1xwND9yrOtBZ75u-wwnmkJUkoUyeBlJvBWKQ,1541
-biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=G-4wNGGZPCEXup1u9dQwSQ6P-oZVRU_faFMoXfAn6i8,7320
+biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=8GtL7ysCacCpnt2vrkAfC47k1N-x3jhUSf-ZxOFIf60,7469
 biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=BN8HSl1HoZp8ibESaCVEJPCBWzmu1AFLMgW5ZeZphS0,3077
 biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=xu256GS80jV8kZePn7qFncK58dYSHzaQY3_SDnuxv6E,3598
 biopipen/scripts/scrna/SeuratClusterStats.R,sha256=ITFqh7p1ggtDXzVxbBEO2TcdOw4dA6oGhL5m7hFAQmU,1838
@@ -284,7 +284,7 @@ biopipen/utils/misc.py,sha256=pDZ-INWVNqHuXYvcjmu8KqNAigkh2lsHy0BxX44CPvc,4048
 biopipen/utils/reference.py,sha256=Oc6IlA1giLxymAuI7DO-IQLHQ7-DbsWzOQE86oTDfMU,5955
 biopipen/utils/reporter.py,sha256=VwLl6xyVDWnGY7NEXyqBlkW8expKJoNQ5iTyZSELf5c,4922
 biopipen/utils/vcf.py,sha256=MmMbAtLUcKPp02jUdk9TzuET2gWSeoWn7xgoOXFysK0,9393
-biopipen-0.34.12.dist-info/METADATA,sha256=r62XsxYiMKsDivaqL_tamLQ5GRnOrI_-3ssfjg9ugcA,1027
-biopipen-0.34.12.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-biopipen-0.34.12.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.34.12.dist-info/RECORD,,
+biopipen-0.34.14.dist-info/METADATA,sha256=uIS3ZdJr3bVM1TspZIe2NmoVavOa_XGKe4qsuRk7gdw,1027
+biopipen-0.34.14.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+biopipen-0.34.14.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.34.14.dist-info/RECORD,,