biopipen 0.29.1__py3-none-any.whl → 0.29.2__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.29.1"
+__version__ = "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/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/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/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/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/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.dist-info → biopipen-0.29.2.dist-info}/METADATA

@@ -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-0.29.1.dist-info → biopipen-0.29.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=QTaZs8dGSlxK5ryfzkJ2KhyNkszMPGsEYfsjGAbckck,23
+biopipen/__init__.py,sha256=f5--I8wu8KDVcUAUM1dKof58bj59kV6atq2ccm3sqPs,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=IL31RfhuF-6V46lvLs1F-Z4SPmUuTvWzk5PN37Xjrqc,1907
@@ -143,15 +143,15 @@ biopipen/scripts/scrna/ExprImputation-alra.R,sha256=w3W1txJcdWg52-SETY2Z0lO7maDN
 biopipen/scripts/scrna/ExprImputation-rmagic.R,sha256=jYIfqZpnvjKJkvItLnemPVtUApHBYQi1_L8rHVbEe1M,735
 biopipen/scripts/scrna/ExprImputation-scimpute.R,sha256=mg40qCUW7-nP5oHPvARq7dmtoahM0GRFWXQpum0BXVk,1082
 biopipen/scripts/scrna/ExprImputation.R,sha256=GcdZJpkDpq88hRQjtLZY5-byp8V43stEFm5T-pQbU6A,319
-biopipen/scripts/scrna/MarkersFinder.R,sha256=WN3YRaU5g58JNN8LB8BLonQg4YAVzxEBpCXNLbtkngs,22894
-biopipen/scripts/scrna/MetaMarkers.R,sha256=9ve1X0TrDzS_ZEW6HtU3n8R-uPx7q-hYMMNFVDSE8wQ,11272
+biopipen/scripts/scrna/MarkersFinder.R,sha256=6CjciBZsVUIjsEe_xpO0s5K-uy2kKa1c76Ks_lndX-g,22950
+biopipen/scripts/scrna/MetaMarkers.R,sha256=xb1dt4N-ra26l6pWmL4Ieix0MB6QOU7CDcxufMZE3Xk,12064
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=JSHd-_-KiFqW8avCGxgU4T-C5BtDr2u0kwIvEu2lFIg,4188
 biopipen/scripts/scrna/RadarPlots.R,sha256=TGPUTUcHOHgd9rsNtLYT-N6WHiFNDBZsiIoqkyAJh0A,13020
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
 biopipen/scripts/scrna/ScFGSEA.R,sha256=2UCTCIydVkPGvn7WP-_fcE7857iKKDxY56-j-ruyO8o,6254
 biopipen/scripts/scrna/Seurat2AnnData.R,sha256=qz4u-B5J3GMwttubnNnByJXreziFbrP5Mak0L0q7eG0,1557
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=gViDgQ8NorYD64iK0FgcODOrDOw0tExZmhuPRuLNp4g,2354
-biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=W7iYhaFsC5EMZLO50QukYPLYGK4bq9kQc1VT5FwvI68,15496
+biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=Cg7fVdDnapS98ak9z2Ha77CLqBkNJ4IYX1q1ssfGNeU,15599
 biopipen/scripts/scrna/SeuratClusterStats-hists.R,sha256=YhuD-GePjJPSkR0iLRgV_hiGHD_bnOIKp-LB6GCwquo,5037
 biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=GVKIXFNS_syCuSN8oxoBkjxxAeI5LdSxh-qLVkUsbDA,2146
 biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=bBbvNCvV6dZLg9zvhh2nR48_53md5A5UEqrPXD00MZU,9263
@@ -170,8 +170,8 @@ biopipen/scripts/scrna/Subset10X.R,sha256=T2nJBTwOe12AIKC2FZsMSv6xx3s-67CYZokpz5
 biopipen/scripts/scrna/TopExpressingGenes.R,sha256=kXMCYHVytgVgO_Uq66fKKFCFV2PPXE8VREy_0yYPLpU,7475
 biopipen/scripts/scrna/celltypist-wrapper.py,sha256=f5M8f4rU5nC7l17RS0YVmUPpLLz4D6PIcgWtA77UExM,1722
 biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
-biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=sOnHSH0Ld-tXSIXJPnXLYgRtEru5M0g3HRxbrHWQ_0U,5170
-biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=RPSxEHWk50Fyw5YPBVVGeWwd55Hi0zjbipLuM5O4tjs,5465
+biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=EFUhI65cPEktZnZquzfVoJcBd_pNcT5jag5XOWHj-Os,5222
+biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=jeTuhWEn2ajL1ZmGpCBy7cBSd1d387P-YetnB6qjhxc,5502
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=95DLX1Rz0tobOuDZ8V9YdGgO0KiNthhccoeeOK21tno,16216
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=rQ9iwGh9FNRZlJJzM4QItdyXmebfzLAq05ZAjb1kGUw,9831
 biopipen/scripts/snp/MatrixEQTL.R,sha256=QPnUW7Rk5UrAQLiBg9FdCItUC26RDBHf7UrfL66dMto,7202
@@ -188,7 +188,7 @@ biopipen/scripts/snp/PlinkUpdateName.py,sha256=sYyb0ek46wRQfclFfoJEhQyQ-zWsFd2xp
 biopipen/scripts/stats/ChowTest.R,sha256=4p7NULmfOZSfeBSQ04els0h3cXOK5yeCJJ4-gEBPOGk,3617
 biopipen/scripts/stats/DiffCoexpr.R,sha256=5hQDV2_7bKdKUsOGMZUa0GS5rc7kFspxonNyFEPmtbc,4516
 biopipen/scripts/stats/LiquidAssoc.R,sha256=s-XJbFoOfH4eWSkxbbOSHZ1x16lY0Sdod_V1KvSkM8k,3727
-biopipen/scripts/stats/Mediation.R,sha256=lqMOrIxRqbEhQipZJ-VE8qQSJn0MI910Vl6DIVyHyNE,2825
+biopipen/scripts/stats/Mediation.R,sha256=jf7ORVbbd9wtEOEJRLowKexQCkOhFmc4v5kkPsNqWpY,3160
 biopipen/scripts/stats/MetaPvalue.R,sha256=fnqayZeHd61cP9PxZZAebg5lE7JQgFG5MElCct43S1M,4012
 biopipen/scripts/stats/MetaPvalue1.R,sha256=falhaOeoa8E7ZbddXfGsSdim5P7eQvA7RFGD7XSrBUk,1733
 biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=Cxh7fiSNCxWDTfIJqZDOOnaSrw-85S_fH2U-PWY03hc,704
@@ -269,7 +269,7 @@ biopipen/utils/reference.py,sha256=oi5evicLwHxF0KAIPNZohBeHJLJQNWFJH0cr2y5pgcg,5
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=pJjYP8bIZpNAtTQ32rOXhZxaM1Y-6D-xUcK3pql9tbk,4316
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.29.1.dist-info/METADATA,sha256=62K0OT3uiUi6Gnt0WGHGaox3WNV7hsbUsg60iPCc4nU,882
-biopipen-0.29.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-biopipen-0.29.1.dist-info/entry_points.txt,sha256=69SbeMaF47Z2DS40yo-qDyoBKmMmumrNnsjEZMOioCE,625
-biopipen-0.29.1.dist-info/RECORD,,
+biopipen-0.29.2.dist-info/METADATA,sha256=9tT8IW-AiQXwRLIzbARle_vaYVL7h5f_wyEwq8ZAHA8,882
+biopipen-0.29.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.29.2.dist-info/entry_points.txt,sha256=69SbeMaF47Z2DS40yo-qDyoBKmMmumrNnsjEZMOioCE,625
+biopipen-0.29.2.dist-info/RECORD,,