biopipen 0.25.2__py3-none-any.whl → 0.25.4__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.25.2"
+__version__ = "0.25.4"

biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R

@@ -189,8 +189,7 @@ if (outtype == "h5ad") {
             sobj,
             celltypist_out[
                 rownames(sobj@meta.data),
-                # setdiff(colnames(celltypist_out), colnames(sobj@meta.data)),
-                ,
+                setdiff(colnames(celltypist_out), colnames(sobj@meta.data)),
                 drop = FALSE
             ]
         )
@@ -217,16 +216,19 @@ if (outtype == "h5ad") {
                     summarise(seurat_clusters = first(seurat_clusters), .groups = "drop") %>%
                     mutate(seurat_clusters = make.unique(seurat_clusters))
                 cluster_map <- split(cluster_map$seurat_clusters, cluster_map$seurat_clusters_id)
-                sobj@meta.data$seurat_clusters <- sobj@meta.data[[over_clustering]]
+                if (over_clustering != "seurat_clusters") {
+                    sobj@meta.data$seurat_clusters <- sobj@meta.data[[over_clustering]]
+                }
                 Idents(sobj) <- "seurat_clusters"
                 cluster_map$object <- sobj
+                log_info("Renaming clusters ...")
                 sobj <- do_call(RenameIdents, cluster_map)
                 sobj@meta.data$seurat_clusters <- Idents(sobj)
-                Idents(sobj) <- "seurat_clusters"
             }
         } else if (!is.null(newcol)) {
             sobj@meta.data[[newcol]] <- sobj@meta.data[["predicted_labels"]]
         }
+        log_info("Saving Seurat object in RDS ...")
         saveRDS(sobj, outfile)
     }
 } else {

biopipen/scripts/scrna/CellsDistribution.R

@@ -25,6 +25,7 @@ cells_n <- {{envs.cells_n | r}}  # nolint
 subset <- {{envs.subset | r}}  # nolint
 descr <- {{envs.descr | r}}  # nolint
 devpars <- {{envs.devpars | r}}  # nolint
+hm_devpars <- {{envs.hm_devpars | r}}  # nolint
 each <- {{envs.each | r}}  # nolint
 section <- {{envs.section | r}}  # nolint
 overlap <- {{envs.overlap | r}}  # nolint
@@ -60,6 +61,7 @@ expand_cases <- function() {
                 cells_orderby = cells_orderby,
                 cells_n = cells_n,
                 devpars = devpars,
+                hm_devpars = hm_devpars,
                 each = each,
                 section = section,
                 subset = subset,
@@ -79,12 +81,14 @@ expand_cases <- function() {
                 cells_orderby = cells_orderby,
                 cells_n = cells_n,
                 devpars = devpars,
+                hm_devpars = hm_devpars,
                 each = each,
                 section = section,
                 subset = subset,
                 descr = descr
             )
             case$devpars <- list_setdefault(case$devpars, devpars)
+            case$hm_devpars <- list_setdefault(case$hm_devpars, hm_devpars)
             filled_cases[[name]] <- case
         }
     }

biopipen/scripts/tcr/Immunarch.R

@@ -57,6 +57,7 @@ rm(meta)
 log_info("Mutating data if `envs.mutaters` is provided ...")
 if (!is.null(mutaters) && length(mutaters) > 0) {
     exdata = mutate(exdata, !!!lapply(mutaters, parse_expr))
+    immdata = immdata_from_expanded(exdata)
 }
 
 n_samples = length(immdata$data)

biopipen/utils/single_cell.R

@@ -55,8 +55,7 @@ filter_expanded_immdata <- function(exdata, filters, update_clones = FALSE) {
     if (length(filters) == 0) {
         return(exdata)
     }
-    out <- exdata %>%
-        dplyr::filter(!!parse_expr(filters))
+    out <- exdata %>% dplyr::filter(!!parse_expr(filters))
     if (update_clones) {
         out <- out %>%
             group_by(Sample, CDR3.aa) %>%
@@ -101,11 +100,13 @@ immdata_from_expanded <- function(
         ),
         function(dat) {
             ncells <- nrow(dat)
+            dat_cols <- setdiff(colnames(dat), c("Clones", "Proportion", cell_id))
             dat %>% group_by(CDR3.aa) %>%
                 summarise(
                     Clones = ifelse(update_clones, n(), first(Clones)),
                     Proportion = ifelse(update_clones, n() / ncells, first(Proportion)),
                     !!sym(cell_id) := paste0(!!sym(cell_id), collapse = ";"),
+                    !!!parse_exprs(sapply(dat_cols, function(x) paste0('first(`', x, '`)'))),
                     .groups = "drop"
                 ) %>%
                 arrange(desc(Clones))

{biopipen-0.25.2.dist-info → biopipen-0.25.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.25.2
+Version: 0.25.4
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -14,7 +14,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Provides-Extra: runinfo
-Requires-Dist: datar[pandas] (>=0.15.3,<0.16.0)
+Requires-Dist: datar[pandas] (>=0.15.4,<0.16.0)
 Requires-Dist: pipen-board[report] (>=0.14,<0.15)
 Requires-Dist: pipen-cli-run (>=0.12,<0.13)
 Requires-Dist: pipen-filters (>=0.11,<0.12)

{biopipen-0.25.2.dist-info → biopipen-0.25.4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=NMzPG-AisbqV0qHNDcM-oIMtdXA6rLhjzeATPyNq6Nw,23
+biopipen/__init__.py,sha256=ecF8WlGgNuYRj3QRbMJQBVjdpKbSFwlW9naM4NJEUOE,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=Rn7Cta7WsMtmQkKGC4h9d5dU_STaIVBgR8UliiGgL6o,1757
@@ -112,13 +112,13 @@ biopipen/scripts/plot/Heatmap.R,sha256=4v_oRME8ZiwczIlBIp-OP_YPWLAvBKzbHiwNBCZ0X
 biopipen/scripts/plot/VennDiagram.R,sha256=GVc-kyHqnXrbXZvy-evcxI1XGtlLSChBiVnMjPywNMA,731
 biopipen/scripts/rnaseq/UnitConversion.R,sha256=9etSQ6ivtlrgSg4mLjViZAl8nUtCxfEROxXvFCpN9sg,1928
 biopipen/scripts/scrna/AnnData2Seurat.R,sha256=16ASr8B7B7tj7hZpwL31v6GASfh8wcBwIDHG-wi5Jec,2534
-biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=vj00tjOXoSZkzq5J1WMDgU7v4ClivnmgVgr-MFSC9M8,8895
+biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=Hzqt-I41ThiSGPzqrg5ma4IQbCDnM1ztfTscPqthdfM,9009
 biopipen/scripts/scrna/CellTypeAnnotation-direct.R,sha256=ST7hJo6IY3-lfj1ymFCxxTH4cAsu8CVTcOKpELBeyuo,1855
 biopipen/scripts/scrna/CellTypeAnnotation-hitype.R,sha256=6_DBAlLKcHqaMyWGZWvTd4gFfHymfz9s2XLja8aj1qA,1869
 biopipen/scripts/scrna/CellTypeAnnotation-sccatch.R,sha256=1ejye0hs-EOwzzdP9gFWSLPcF6dOAA6VmNKXEjmS11E,1654
 biopipen/scripts/scrna/CellTypeAnnotation-sctype.R,sha256=1nKRtzhVoJ9y0yMg1sgI6u7czsrk2cN0FvNUCZo8l-o,3878
 biopipen/scripts/scrna/CellTypeAnnotation.R,sha256=OwLM_G4D7TG4HhIJjQxgIQM92X86lsWp9MVyXTTkLSc,618
-biopipen/scripts/scrna/CellsDistribution.R,sha256=r9XJwA-VZ2JP8TZEe4OS8Ah1b06yd58HrfAyPi4Be1M,16562
+biopipen/scripts/scrna/CellsDistribution.R,sha256=zoTE0vO5qcMY1PxwGlNi9eY1F50n1XMc8o0AUzdDN68,16768
 biopipen/scripts/scrna/DimPlots.R,sha256=-mXOTMnpPxvR30XLjwcohFfFx7xTqWKKiICwJiD6yEo,1554
 biopipen/scripts/scrna/ExprImpution-alra.R,sha256=w3W1txJcdWg52-SETY2Z0lO7maDNfiMjBYIGN587YW0,843
 biopipen/scripts/scrna/ExprImpution-rmagic.R,sha256=jYIfqZpnvjKJkvItLnemPVtUApHBYQi1_L8rHVbEe1M,735
@@ -175,7 +175,7 @@ biopipen/scripts/tcr/Immunarch-overlap.R,sha256=GVt-qJPtd6NEe5njAqNStf2AP6pLkv7I
 biopipen/scripts/tcr/Immunarch-spectratyping.R,sha256=jm8qI_A6HBgr1RT6-kq13z46_3aXHwz_LbQk4Ggeq9Y,2882
 biopipen/scripts/tcr/Immunarch-tracking.R,sha256=0tiywpGhd3H0REp4xrhOlkWzJM4ntrQjrVesHbEWT40,4374
 biopipen/scripts/tcr/Immunarch-vjjunc.R,sha256=vSVPdRPSlpAfuX4ynA2UjfUC0_61yMAaPieJM-5J4sw,4434
-biopipen/scripts/tcr/Immunarch.R,sha256=FVPK5qu6twSSJJNDCAZO4wNned6uIOBZHgBNeIgLmKw,3037
+biopipen/scripts/tcr/Immunarch.R,sha256=SKgdTGCDBJnWMzKInfljJiOlCrQk07ab3EqS2GpgyFE,3081
 biopipen/scripts/tcr/Immunarch2VDJtools.R,sha256=QB9ILGbnsfoWaRANK6ceb14wpSWy8F1V1EdEmfIqiks,706
 biopipen/scripts/tcr/ImmunarchFilter.R,sha256=o25O36FwH_0w6F8DFQ0SfpcwDzlzaGefXqr9ESrvb4k,3974
 biopipen/scripts/tcr/ImmunarchLoading.R,sha256=l_l-gojiCKI_MWgIUe2zG5boVtNipBv4rACRJEcrnFE,5734
@@ -225,9 +225,9 @@ biopipen/utils/mutate_helpers.R,sha256=Bqy6Oi4rrPEPJw0Jq32bVAwwBfZv7JJL9jFcK5x-c
 biopipen/utils/plot.R,sha256=pzl37PomNeUZPxohHZ2w93j3Fc4T0Qrc62FF-9MTKdw,4417
 biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4420
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
-biopipen/utils/single_cell.R,sha256=bKduqOQjSC8BtZJuwfUShR49omoEMbB57n3Gi6dYlqA,4147
+biopipen/utils/single_cell.R,sha256=pJjYP8bIZpNAtTQ32rOXhZxaM1Y-6D-xUcK3pql9tbk,4316
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.25.2.dist-info/METADATA,sha256=k3E_YX4GeDSwCwjTh7fyG_UivPes67k5_S_rXqENt50,932
-biopipen-0.25.2.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-biopipen-0.25.2.dist-info/entry_points.txt,sha256=O7K7PHoJi-4tERYpqmryuTvrFNEsptMpqliZzB2oBQQ,577
-biopipen-0.25.2.dist-info/RECORD,,
+biopipen-0.25.4.dist-info/METADATA,sha256=gM8icW3uqM9GhZn0A1RNHSopuBteumXJMAKkmnRgUoQ,932
+biopipen-0.25.4.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+biopipen-0.25.4.dist-info/entry_points.txt,sha256=O7K7PHoJi-4tERYpqmryuTvrFNEsptMpqliZzB2oBQQ,577
+biopipen-0.25.4.dist-info/RECORD,,