biopipen 0.34.13__py3-none-any.whl → 0.34.15__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.34.13"
+__version__ = "0.34.15"

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

@@ -600,6 +600,28 @@ run_case <- function(name) {
 
             if (length(allenrich_plots) > 0 && !is.null(enriches) && nrow(enriches) > 0) {
                 log$info("- Visualizing all enrichments together ...")
+                # add other metadata columns if any by mapping groupname
+                # only add the metadata columns from object if there is a single value mapped
+                metacols <- srtobj@meta.data %>% group_by(!!sym(each)) %>%
+                    summarize(across(everything(), ~ n_distinct(.) == 1), .groups = "keep") %>%
+                    select(where(~ all(. == TRUE))) %>%
+                    colnames()
+
+                if (length(metacols) > 1) {
+                    metadf <- srtobj@meta.data[, metacols, drop = FALSE]  %>%
+                        distinct(!!sym(each), .keep_all = TRUE)
+
+                    for (col in setdiff(metacols, each)) {
+                        if (col %in% colnames(enriches)) {
+                            warning("Column name conflict: {col}, adding with suffix '_meta'", immediate. = TRUE)
+                            metadf[[paste0(col, "_meta")]] <- metadf[[col]]
+                            metadf[[col]] <- NULL
+                        }
+                    }
+
+                    enriches <- left_join(enriches, metadf, by = each)
+                }
+
                 process_allenriches(enriches, allenrich_plots, name, each)
             }
         }
@@ -607,8 +629,14 @@ run_case <- function(name) {
         return(invisible())
     }
 
-    case$object <- if (is.null(subset_)) srtobj else filter(srtobj, !!parse_expr(subset_))
+    # Let RunSeuratDEAnalysis handle the subset
+    case$subset <- subset_
+    case$object <- srtobj
     markers <- do_call(RunSeuratDEAnalysis, case)
+    case$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]]))
@@ -621,7 +649,7 @@ run_case <- function(name) {
 
             attr(ident_markers, "ident_1") <- ident
             enrich <- process_markers(ident_markers, info = info, case = list(
-                object = case$object,
+                object = subobj,
                 dbs = dbs,
                 group_by = case$group_by,
                 sigmarkers = sigmarkers,
@@ -638,7 +666,7 @@ run_case <- function(name) {
             log$info("- Visualizing all markers together ...")
             process_allmarkers(
                 markers,
-                object = case$object,
+                object = subobj,
                 comparison_by = case$group_by,
                 plotcases = allmarker_plots,
                 casename = name,
@@ -653,12 +681,35 @@ run_case <- function(name) {
 
         if (length(allenrich_plots) > 0) {
             log$info("- Visualizing all enrichments together ...")
+            # add other metadata columns if any by mapping groupname
+            # only add the metadata columns from object if there is a single value mapped
+            metacols <- subobj@meta.data %>% group_by(!!sym(case$group_by)) %>%
+                summarize(across(everything(), ~ n_distinct(.) == 1), .groups = "keep") %>%
+                select(where(~ all(. == TRUE))) %>%
+                colnames()
+
+            if (length(metacols) > 1) {
+                metadf <- subobj@meta.data[, metacols, drop = FALSE]  %>%
+                    distinct(!!sym(case$group_by), .keep_all = TRUE)
+
+                for (col in setdiff(metacols, case$group_by)) {
+                    if (col %in% colnames(enriches[[1]])) {
+                        warning("Column name conflict: {col}, adding with suffix '_meta'", immediate. = TRUE)
+                        metadf[[paste0(col, "_meta")]] <- metadf[[col]]
+                        metadf[[col]] <- NULL
+                    }
+                }
+
+                for (ne in names(enriches)) {
+                    enriches[[ne]] <- left_join(enriches[[ne]], metadf, by = case$group_by)
+                }
+            }
             process_allenriches(enriches, allenrich_plots, name, case$group_by)
         }
     } else {
         info <- case_info(name, outdir, create = TRUE)
         enrich <- process_markers(markers, info = info, case = list(
-            object = case$object,
+            object = subobj,
             dbs = dbs,
             group_by = case$group_by,
             sigmarkers = sigmarkers,

{biopipen-0.34.13.dist-info → biopipen-0.34.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: biopipen
-Version: 0.34.13
+Version: 0.34.15
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.34.13.dist-info → biopipen-0.34.15.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=wgMjsjpJp94VKXjF2z1Lam_lUNV2X8aqhQOuo-pcpZg,24
+biopipen/__init__.py,sha256=Rz3xEpDF80HTbA8ImEKPXgpJjUW3trCJqVbTVpBlx44,24
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=lZV_vbYWk6uqm19ZWJcsZCcSNqAdIfN2fOfamzxZpg4,2148
@@ -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=4SVcjG9GjR_WvKjkbOsu0GBDUkFTIqo2z45_gqUhqog,26187
+biopipen/scripts/scrna/MarkersFinder.R,sha256=SBh3cA2WZQIlZTysAlU-U9knzO9gU0XW-yi8mk2iJG4,28588
 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
@@ -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-0.34.13.dist-info/METADATA,sha256=0G3Xs0cXYh9cnRf4y8g7rjznqdxB_VxqfZUEiEK3bfo,1027
-biopipen-0.34.13.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-biopipen-0.34.13.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.34.13.dist-info/RECORD,,
+biopipen-0.34.15.dist-info/METADATA,sha256=ArJuTPoapr8eXqqyw0QMZkzalGdJLJED0QpmttmNSA0,1027
+biopipen-0.34.15.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+biopipen-0.34.15.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.34.15.dist-info/RECORD,,