biopipen 0.25.2__tar.gz → 0.25.4__tar.gz

{biopipen-0.25.2 → biopipen-0.25.4}/PKG-INFO

@@ -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-0.25.4/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.25.4"

{biopipen-0.25.2 → biopipen-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-0.25.2 → biopipen-0.25.4}/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-0.25.2 → biopipen-0.25.4}/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-0.25.2 → biopipen-0.25.4}/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 → biopipen-0.25.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.25.2"
+version = "0.25.4"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"
@@ -16,7 +16,7 @@ pipen-filters = "^0.11"
 pipen-cli-run = "^0.12"
 pipen-verbose = "^0.10"
 pipen-poplog = "^0.0.2"
-datar = { version = "^0.15.3", extras = ["pandas"] }
+datar = { version = "^0.15.4", extras = ["pandas"] }
 pipen-board = { version = "^0.14", extras = ["report"] }
 pipen-runinfo = { version = "^0.5", optional = true }
 

{biopipen-0.25.2 → biopipen-0.25.4}/setup.py

@@ -42,7 +42,7 @@ package_data = \
               'scripts/tcr/*']}
 
 install_requires = \
-['datar[pandas]>=0.15.3,<0.16.0',
+['datar[pandas]>=0.15.4,<0.16.0',
  'pipen-board[report]>=0.14,<0.15',
  'pipen-cli-run>=0.12,<0.13',
  'pipen-filters>=0.11,<0.12',
@@ -77,7 +77,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.25.2',
+    'version': '0.25.4',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.25.2/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.25.2"