biopipen 0.29.1__tar.gz → 0.29.2__tar.gz

{biopipen-0.29.1 → biopipen-0.29.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.29.1
+Version: 0.29.2
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.29.2/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.29.2"

{biopipen-0.29.1 → biopipen-0.29.2}/biopipen/scripts/scrna/MarkersFinder.R

@@ -70,7 +70,8 @@ if (defassay == "SCT" && !"PrepSCTFindMarkers" %in% names(srtobj@commands)) {
 
     srtobj <- PrepSCTFindMarkers(srtobj)
     # compose a new SeuratCommand to record it to srtobj@commands
-    scommand <- srtobj@commands$FindClusters
+    commands <- names(srtobj@commands)
+    scommand <- srtobj@commands[[commands[length(commands)]]]
     scommand@name <- "PrepSCTFindMarkers"
     scommand@time.stamp <- Sys.time()
     scommand@assay.used <- "SCT"

{biopipen-0.29.1 → biopipen-0.29.2}/biopipen/scripts/scrna/MetaMarkers.R

@@ -36,6 +36,20 @@ set.seed(8525)
 
 log_info("- Reading Seurat object ...")
 srtobj <- readRDS(srtfile)
+if (DefaultAssay(srtobj) == "SCT" && !"PrepSCTFindMarkers" %in% names(srtobj@commands)) {
+    log_warn("- SCTransform used but PrepSCTFindMarkers not applied, running ...")
+
+    srtobj <- PrepSCTFindMarkers(srtobj)
+    # compose a new SeuratCommand to record it to srtobj@commands
+    commands <- names(srtobj@commands)
+    scommand <- srtobj@commands[[commands[length(commands)]]]
+    scommand@name <- "PrepSCTFindMarkers"
+    scommand@time.stamp <- Sys.time()
+    scommand@assay.used <- "SCT"
+    scommand@call.string <- "PrepSCTFindMarkers(object = srtobj)"
+    scommand@params <- list()
+    srtobj@commands$PrepSCTFindMarkers <- scommand
+}
 
 log_info("- Mutate meta data if needed ...")
 if (!is.null(mutaters) && length(mutaters)) {
@@ -79,13 +93,13 @@ expand_each <- function(name, case) {
             by = make.names(paste0("..", name, "_", case$each, "_", each))
             idents <- case$idents
             if (is.null(idents) || length(idents) == 0) {
-                srtobj@meta.data = srtobj@meta.data %>%
+                srtobj@meta.data <<- srtobj@meta.data %>%
                     mutate(
                         !!sym(by) := if_else(!!sym(case$each) == each, !!sym(case$group_by), NA)
                     )
                 idents <- srtobj@meta.data %>% pull(case$group_by) %>% unique() %>% na.omit()
             } else {
-                srtobj@meta.data = srtobj@meta.data %>%
+                srtobj@meta.data <<- srtobj@meta.data %>%
                     mutate(
                         !!sym(by) := if_else(
                             !!sym(case$each) == each & !!sym(case$group_by) %in% case$idents,
@@ -204,6 +218,10 @@ do_case <- function(casename) {
         if (is.null(df)) {
             msg <- "No markers found. May be due to too few cells or features."
         } else {
+            df <- df[
+                apply(df, 1, function(x) !all(is.na(x)) && !all(x == x[1])), ,
+                drop = FALSE
+            ]
             genes <- rownames(df)
             # rows: cells, cols: genes
             df <- cbind(as.data.frame(scale(Matrix::t(df))), sobj@meta.data[, case$group_by])

{biopipen-0.29.1 → biopipen-0.29.2}/biopipen/scripts/scrna/SeuratClusterStats-features.R

@@ -75,6 +75,7 @@ do_one_features = function(name) {
         Idents(case$object) = case$ident
     }
     n_uidents = length(unique(Idents(case$object)))
+    max_nchar_idents = max(nchar(unique(as.character(Idents(case$object)))))
 
     fn = NULL
     default_devpars = NULL
@@ -97,13 +98,14 @@ do_one_features = function(name) {
         case$kind = "violin"
         if (is.null(case$cols)) { case$cols = pal_biopipen()(n_uidents) }
         if (is.null(case$pt.size)) { case$pt.size = 0 }
+
         excluded_args = c(excluded_args, "reduction")
         fn = VlnPlot
         default_devpars = function(features, ncol) {
             if (is.null(ncol)) { ncol = 1 }
             list(
                 width = 400 * ncol,
-                height = ceiling(length(features) / ncol) * 200,
+                height = ceiling(length(features) / ncol + max_nchar_idents * .05) * 150,
                 res = 100
             )
         }

{biopipen-0.29.1 → biopipen-0.29.2}/biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R

@@ -139,8 +139,11 @@ do_one_subset <- function(s, subset_col, subset_prefix) {
     if (any(unlist(lapply(x, class)) == "try-error")) {
         stop("mclapply error")
     }
-
-    for (r in x) { do.call(add_report, r) }
+    for (r in x) {
+        if (!is.null(r)) {
+            do.call(add_report, r)
+        }
+    }
 }
 
 do_one_subset_col <- function(subset_col, subset_prefix) {

{biopipen-0.29.1 → biopipen-0.29.2}/biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R

@@ -184,6 +184,10 @@ if (ncores == 1) {
     }
 }
 report = unlist(x, recursive = FALSE)
-for (r in report) { do.call(add_report, r) }
+for (r in report) {
+    if (!is.null(r)) {
+        do.call(add_report, r)
+    }
+}
 
 save_report(joboutdir)

{biopipen-0.29.1 → biopipen-0.29.2}/biopipen/scripts/stats/Mediation.R

@@ -35,9 +35,20 @@ if (!is.null(fmlfile)) {
 
 args <- args %||% list()
 
-medanalysis = function(casename) {
+medanalysis <- function(i, total) {
+    casename <- names(cases)[i]
     case <- cases[[casename]]
-    log_info("- Case:", casename)
+    if (total < 50) {
+        log_info("- Case: ", casename)
+    } else if (total < 500) {
+        if (i %% 10 == 0) {
+            log_info("- Processing case {i}/{total} ...")
+        }
+    } else {
+        if (i %% 100 == 0) {
+            log_info("- Processing case {i}/{total} ...")
+        }
+    }
     M <- case$M
     Y <- case$Y
     X <- case$X
@@ -85,7 +96,8 @@ medanalysis = function(casename) {
     }
 }
 
-out <- do_call(rbind, mclapply(names(cases), medanalysis, mc.cores = ncores))
+total <- length(cases)
+out <- do_call(rbind, mclapply(1:total, medanalysis, total = total, mc.cores = ncores))
 
 if (padj != "none") {
     out$Padj <- p.adjust(out$Pval, method = padj)

{biopipen-0.29.1 → biopipen-0.29.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.29.1"
+version = "0.29.2"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.29.1 → biopipen-0.29.2}/setup.py

@@ -82,7 +82,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.29.1',
+    'version': '0.29.2',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.29.1/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.29.1"