biopipen 0.34.0__py3-none-any.whl → 0.34.2__py3-none-any.whl

biopipen/scripts/scrna/ScFGSEA.R

@@ -7,9 +7,9 @@ srtfile <- {{in.srtobj | r}}  # nolint
 outdir <- {{out.outdir | r}}  # nolint
 joboutdir <- {{job.outdir | r}}  # nolint
 mutaters <- {{envs.mutaters | r}}  # nolint
-group.by <- {{envs["group-by"] | r}}  # nolint
-ident.1 <- {{envs["ident-1"] | r}}  # nolint
-ident.2 <- {{envs["ident-2"] | r}}  # nolint
+group_by <- {{envs.group_by | default: envs["group-by"] | default: None | r}}  # nolint
+ident_1 <- {{envs.ident_1 | default: envs["ident-1"] | default: None | r}}  # nolint
+ident_2 <- {{envs.ident_2 | default: envs["ident-2"] | default: None | r}}  # nolint
 each <- {{envs.each | r}}  # nolint
 subset <- {{envs.subset | r}}  # nolint
 gmtfile <- {{envs.gmtfile | r}}  # nolint
@@ -18,6 +18,8 @@ top <- {{envs.top | r}}  # nolint
 minsize <- {{envs.minSize | default: envs.minsize | r}}  # nolint
 maxsize <- {{envs.maxSize | default: envs.maxsize | r}}  # nolint
 eps <- {{envs.eps | r}}  # nolint
+alleach_plots_defaults <- {{envs.alleach_plots_defaults | r}}  # nolint
+alleach_plots <- {{envs.alleach_plots | r}}  #
 ncores <- {{envs.ncores | r}}  # nolint
 rest <- {{envs.rest | r: todot="-"}}  # nolint
 cases <- {{envs.cases | r: todot="-"}}  # nolint
@@ -25,6 +27,10 @@ cases <- {{envs.cases | r: todot="-"}}  # nolint
 log <- get_logger()
 reporter <- get_reporter()
 
+alleach_plots <- lapply(alleach_plots, function(x) {
+    list_update(alleach_plots_defaults, x)
+})
+
 log$info("Reading Seurat object ...")
 srtobj <- read_obj(srtfile)
 if (!"Identity" %in% colnames(srtobj@meta.data)) {
@@ -37,9 +43,9 @@ if (!is.null(mutaters) && length(mutaters) > 0) {
 }
 
 defaults <- list(
-    group.by = group.by,
-    ident.1 = ident.1,
-    ident.2 = ident.2,
+    group_by = group_by,
+    ident_1 = ident_1,
+    ident_2 = ident_2,
     each = each,
     subset = subset,
     gmtfile = gmtfile,
@@ -48,6 +54,8 @@ defaults <- list(
     minsize = minsize,
     maxsize = maxsize,
     eps = eps,
+    alleach_plots_defaults = alleach_plots_defaults,
+    alleach_plots = alleach_plots,
     ncores = ncores,
     rest = rest
 )
@@ -55,9 +63,13 @@ defaults <- list(
 expand_each <- function(name, case) {
     outcases <- list()
 
-    case$group.by <- case$group.by %||% "Identity"
+    case$group_by <- case$group_by %||% "Identity"
 
     if (is.null(case$each) || is.na(case$each) || nchar(case$each) == 0 || isFALSE(each)) {
+        if (length(case$alleach_plots) > 0) {
+            stop("Cannot perform `alleach_plots` without `each` defined.")
+        }
+
         outcases[[name]] <- case
     } else {
         eachs <- if (!is.null(case$subset)) {
@@ -77,10 +89,13 @@ expand_each <- function(name, case) {
             newname <- paste0(case$each, "::", each)
             newcase <- case
 
-            newcase$original_case <- name
+            newcase$original_case <- paste0(name, " (all ", case$each,")")
             newcase$each_name <- case$each
             newcase$each <- each
 
+            newcase$alleach_plots_defaults <- NULL
+            newcase$alleach_plots <- NULL
+
             if (!is.null(case$subset)) {
                 newcase$subset <- paste0(case$subset, " & ", bQuote(case$each), " == '", each, "'")
             } else {
@@ -89,6 +104,18 @@ expand_each <- function(name, case) {
 
             outcases[[newname]] <- newcase
         }
+
+        if (length(case$alleach_plots) > 0) {
+            newcase <- case
+
+            newcase$gseas <- list()
+            newcase$alleach_plots <- lapply(
+                newcase$alleach_plots,
+                function(x) { list_update(newcase$alleach_plots_defaults, x) }
+            )
+
+            outcases[[paste0(name, " (all ", case$each,")")]] <- newcase
+        }
     }
     outcases
 }
@@ -108,21 +135,59 @@ ensure_sobj <- function(expr, allow_empty) {
     })
 }
 
-
 do_case <- function(name) {
     log$info("- Processing case: {name} ...")
     case <- cases[[name]]
     info <- case_info(name, outdir, create = TRUE)
 
+    if (!is.null(case$gseas)) {
+
+        each_levels <- names(case$gseas)
+        gseas <- do_call(rbind, lapply(each_levels, function(x) {
+            gsea_df <- case$gseas[[x]]
+            if (nrow(gsea_df) > 0) {
+                gsea_df[[case$each]] <- x
+            } else {
+                gsea_df[[case$each]] <- character(0)  # Empty case
+            }
+            gsea_df
+        }))
+        gseas[[case$each]] <- factor(gseas[[case$each]], levels = each_levels)
+
+        for (plotname in names(case$alleach_plots)) {
+            plotargs <- case$alleach_plots[[plotname]]
+            plotargs <- extract_vars(plotargs, "devpars")
+            plotargs$gsea_results <- gseas
+            plotargs$group_by <- case$each
+            if (plotargs$plot_type == "heatmap") {
+                plotargs$show_row_names <- plotargs$show_row_names %||% TRUE
+                plotargs$show_column_names <- plotargs$show_column_names %||% TRUE
+            }
+
+            p <- do_call(VizGSEA, plotargs)
+
+            outprefix <- file.path(info$prefix, paste0("all.", slugify(plotname)))
+            save_plot(p, outprefix, devpars, formats = "png")
+            reporter$add2(
+                list(kind = "descr", content = paste0("Pathways for all ", case$each, ".")),
+                list(kind = "image", src = paste0(outprefix, ".png")),
+                hs = c(info$section, info$name),
+                hs2 = plotname
+            )
+        }
+
+        return(invisible(NULL))
+    }
+
     allow_empty = !is.null(case$each)
     # prepare expression matrix
     log$info("  Preparing expression matrix...")
-    sobj <- ensure_sobj({ srtobj %>% filter(!is.na(!!sym(case$group.by))) }, allow_empty)
+    sobj <- ensure_sobj({ srtobj %>% filter(!is.na(!!sym(case$group_by))) }, allow_empty)
     if (is.null(sobj)) {
         reporter$add2(
             list(
                 kind = "error",
-                content = paste0("No cells with non-NA `", case$group.by, "` in the Seurat object.")
+                content = paste0("No cells with non-NA `", case$group_by, "` in the Seurat object.")
             ),
             hs = c(info$section, info$name)
         )
@@ -135,20 +200,20 @@ do_case <- function(name) {
             reporter$add2(
                 list(
                     kind = "error",
-                    content = paste0("No cells with non-NA `", case$group.by, "` in the Seurat object.")
+                    content = paste0("No cells with non-NA `", case$group_by, "` in the Seurat object.")
                 ),
                 hs = c(info$section, info$name)
             )
             return(NULL)
         }
     }
-    if (!is.null(case$ident.2)) {
-        sobj <- ensure_sobj({ sobj %>% filter(!!sym(case$group.by) %in% c(case$ident.1, case$ident.2)) }, allow_empty)
+    if (!is.null(case$ident_2)) {
+        sobj <- ensure_sobj({ sobj %>% filter(!!sym(case$group_by) %in% c(case$ident_1, case$ident_2)) }, allow_empty)
         if (is.null(sobj)) {
             reporter$add2(
                 list(
                     kind = "error",
-                    content = paste0("No cells with non-NA `", case$group.by, "` in the Seurat object.")
+                    content = paste0("No cells with non-NA `", case$group_by, "` in the Seurat object.")
                 ),
                 hs = c(info$section, info$name)
             )
@@ -156,20 +221,20 @@ do_case <- function(name) {
         }
     }
 
-    allclasses <- sobj@meta.data[, case$group.by, drop = TRUE]
-    if (is.null(case$ident.2)) {
-        case$ident.2 <- "Other"
-        allclasses[allclasses != case$ident.1] <- "Other"
+    allclasses <- sobj@meta.data[, case$group_by, drop = TRUE]
+    if (is.null(case$ident_2)) {
+        case$ident_2 <- "Other"
+        allclasses[allclasses != case$ident_1] <- "Other"
     }
     exprs <- GetAssayData(sobj, layer = "data")
 
     # get preranks
     log$info("  Getting preranks...")
-    ranks <- RunGSEAPreRank(exprs, allclasses, case$ident.1, case$ident.2, case$method)
+    ranks <- RunGSEAPreRank(exprs, allclasses, case$ident_1, case$ident_2, case$method)
     write.table(
-        ranks,
-        file.path(info$prefix, "fgsea.rank"),
-        row.names = FALSE,
+        as.data.frame(ranks),
+        file.path(info$prefix, "fgsea.rank.txt"),
+        row.names = TRUE,
         col.names = TRUE,
         sep = "\t",
         quote = FALSE
@@ -216,15 +281,17 @@ do_case <- function(name) {
         quote = FALSE
     )
 
+    aspect.ratio <- sqrt(case$top) / sqrt(10)
     p_summary <- VizGSEA(
         result,
         plot_type = "summary",
-        top_term = case$top
+        top_term = case$top,
+        aspect.ratio = aspect.ratio
     )
     save_plot(
         p_summary,
         file.path(info$prefix, "summary"),
-        devpars = list(res = 100, height = attr(p_summary, "height") * 100, width = attr(p_summary, "width") * 100),
+        devpars = list(res = 100, height = attr(p_summary, "height") * 100 / 1.5, width = attr(p_summary, "width") * 100),
         formats = "png"
     )
 
@@ -243,13 +310,13 @@ do_case <- function(name) {
 
     reporter$add2(
         list(
-            name = "Table",
+            name = paste0("Table (", case$ident_1, " vs ", case$ident_2, ")"),
             contents = list(
                 list(kind = "descr", content = paste0(
                     "Showing top 50 pathways by padj in descending order. ",
                     "Use 'Download the entire data' button to download all pathways."
                 )),
-                list(kind = "table", src = file.path(info$prefix, "fgsea"), data = list(nrows = 50))
+                list(kind = "table", src = file.path(info$prefix, "fgsea.tsv"), data = list(nrows = 50))
             )
         ),
         list(
@@ -269,8 +336,14 @@ do_case <- function(name) {
         hs = c(info$section, info$name),
         ui = "tabs"
     )
+
+    if (!is.null(case$original_case) && !is.null(cases[[case$original_case]])) {
+        cases[[case$original_case]]$gseas[[case$each]] <<- result
+    }
+
+    invisible()
 }
 
-sapply(sort(names(cases)), function(name) do_case(name))
+sapply(names(cases), function(name) do_case(name))
 
 reporter$save(joboutdir)

biopipen/scripts/scrna/SeuratClusterStats-features.R

@@ -53,6 +53,10 @@ hvf <- NULL
         }
     }
 
+    if (is.list(features)) {
+        return(lapply(features, function(x) {.get_features(x, object) }))
+    }
+
     return (trimws(unlist(strsplit(features, ","))))
 }
 

biopipen/scripts/scrna/TopExpressingGenes.R

@@ -9,7 +9,7 @@ outdir <- {{out.outdir | r}}
 joboutdir <- {{job.outdir | r}}
 mutaters <- {{ envs.mutaters | r }}
 ident <- {{ envs.ident | r }}
-group.by <- {{ envs["group-by"] | r }}  # nolint
+group_by <- {{ envs.group_by | default: envs["group-by"] | default: None | r }}  # nolint
 each <- {{ envs.each | r }}
 dbs <- {{ envs.dbs | r }}
 n <- {{ envs.n | r }}
@@ -41,7 +41,7 @@ enrich_plots <- lapply(enrich_plots, function(x) {
 })
 defaults <- list(
     ident = ident,
-    group.by = group.by,
+    group_by = group_by,
     each = each,
     dbs = dbs,
     n = n,
@@ -144,7 +144,9 @@ process_markers <- function(markers, info, case) {
                 p <- do_call(VizEnrichment, plotargs)
 
                 outprefix <- file.path(info$prefix, paste0("enrich.", slugify(db), ".", slugify(plotname)))
-                attr(p, "height") <- attr(p, "height") / 1.5
+                if (plotargs$plot_type == "bar") {
+                    attr(p, "height") <- attr(p, "height") / 1.5
+                }
                 save_plot(p, outprefix, plotargs$devpars, formats = "png")
                 plots[[length(plots) + 1]] <- reporter$image(outprefix, c(), FALSE)
             }
@@ -169,17 +171,17 @@ run_case <- function(name) {
     } else {
         subobj <- srtobj
     }
-    case$group.by <- case$group.by %||% "Identity"
+    case$group_by <- case$group_by %||% "Identity"
     if (is.null(case$ident)) {
-        case$ident <- as.character(unique(subobj@meta.data[[case$group.by]]))
+        case$ident <- as.character(unique(subobj@meta.data[[case$group_by]]))
     }
     avgexpr <- AverageExpression(
         subobj,
-        group.by = case$group.by,
+        group_by = case$group_by,
         assays = assay
     )[[assay]]
     # https://github.com/satijalab/seurat/issues/7893
-    colnames(avgexpr) <- as.character(unique(subobj@meta.data[[case$group.by]]))
+    colnames(avgexpr) <- as.character(unique(subobj@meta.data[[case$group_by]]))
     avgexpr <- avgexpr[, case$ident, drop = FALSE]
 
     for (idt in case$ident) {

biopipen/scripts/tcr/ClonalStats.R

@@ -7,7 +7,7 @@ library(biopipen.utils)
 screpfile <- {{in.screpfile | r}}
 outdir <- {{out.outdir | r}}
 joboutdir <- {{job.outdir | r}}
-envs <- {{envs | r}}
+envs <- {{envs | r: todot="-"}}
 mutaters <- envs$mutaters
 cases <- envs$cases
 envs$mutaters <- NULL

biopipen/scripts/tcr/ScRepCombiningExpression.R

@@ -7,7 +7,7 @@ srtobjfile <- {{in.srtobj | r}}
 outfile <- {{out.outfile | r}}
 cloneCall <- {{envs.cloneCall | r}}
 chain <- {{envs.chain | r}}
-group.by <- {{envs["group-by"] | r}}
+group_by <- {{envs.group_by | default: envs["group-by"] | default: None | r}}
 proportion <- {{envs.proportion | r}}
 filterNA <- {{envs.filterNA | r}}
 cloneSize <- {{envs.cloneSize | r}}
@@ -28,7 +28,7 @@ obj <- combineExpression(
     sc.data = srtobj,
     cloneCall = cloneCall,
     chain = chain,
-    group.by = group.by,
+    group.by = group_by,
     proportion = proportion,
     filterNA = filterNA,
     cloneSize = unlist(cloneSize),

{biopipen-0.34.0.dist-info → biopipen-0.34.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: biopipen
-Version: 0.34.0
+Version: 0.34.2
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.34.0.dist-info → biopipen-0.34.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=7wgjZxPxspP87CI4mDkFQuldkKgENXO5FaPiS8EXM88,23
+biopipen/__init__.py,sha256=NtTwQ_23yhWzaTLoJ9fdSclacR1T9pyG3ntupTpaz6g,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=lZV_vbYWk6uqm19ZWJcsZCcSNqAdIfN2fOfamzxZpg4,2148
@@ -22,12 +22,12 @@ biopipen/ns/plot.py,sha256=N41_izb6zi-XArUly5WhLebapNXbTNSgGlOCCwtrDlY,18282
 biopipen/ns/protein.py,sha256=YJtlKoHI2p5yHdxKeQnNtm5QrbxDGOq1UXOdt_7tlTs,6391
 biopipen/ns/regulatory.py,sha256=gJjGVpJrdv-rg2t5UjK4AGuvtLNymaNYNvoD8PhlbvE,15929
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=Ip0Kc2TEtlCqbWYpkLbY6T90Bz32pMoCoVjQB8K7zw8,128961
+biopipen/ns/scrna.py,sha256=1z-PUPkQ6FpfC8RHWtuG8Mvw7w6zmI-Z3shkzO8cekY,143767
 biopipen/ns/scrna_metabolic_landscape.py,sha256=Q95KkHg5jC6eUMSUH-wioPxOzuArP59j3CPsfDTCBM0,22096
 biopipen/ns/snp.py,sha256=iXWrw7Lmhf4_ct57HGT7JGTClCXUD4sZ2FzOgsC2pTg,28123
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
-biopipen/ns/tcr.py,sha256=Gzoz2FIFmeq_--6ppKVt26kjnPHnWHWAzdj1YvBhrRk,99036
+biopipen/ns/tcr.py,sha256=dw6zEm5FNzf5ViVNxX81YwlzmXSAwWszxk6OL4Yh5p0,99036
 biopipen/ns/vcf.py,sha256=zjOH2qiSJsHACLmBqV-Tew-mn-peZgvYLAWjTLh7uTI,23823
 biopipen/ns/web.py,sha256=8VY4Xsb8UrzS4IkGUX_84GQP1JG6NcTZrV7f9tA1tUI,5458
 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
@@ -51,8 +51,6 @@ biopipen/reports/scrna/DimPlots.svelte,sha256=ubIx8dgppzSB8WS_B4LN2T3bOTerP4Ck6o
 biopipen/reports/scrna/MarkersFinder.svelte,sha256=77rD1psj0VJykPDhfwS-B8mubvaasREAE6RYR2atTN4,444
 biopipen/reports/scrna/MetaMarkers.svelte,sha256=iIFRKjvVYrM1AtDWqq8UfeS8q23R8FKg2yepKAw2KSE,508
 biopipen/reports/scrna/RadarPlots.svelte,sha256=g_fp9d3vdnzk-egXPhkhhfWXOeG569Rj8rYLRIKmlLc,396
-biopipen/reports/scrna/ScFGSEA.svelte,sha256=Gqt-XjqsB3XgdR3XukvphwyMExZpScwqgEo7AD-gK6g,491
-biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=tt5_Vjym4coFT8Bvz0s6ZcCioTOIwCj83jdCGqPCmUw,491
 biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=1RC-FuYr_M1xInPaNrEGyzPQGy2d1rZjYdKPfLAOPUs,2346
 biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=VTU-D8iELO7zzK5cJg7oZTna2wu4O_gJ8d7G8N7Veg8,5473
 biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=Fr9_DJPuv2hzac-zzqtVBir-FXwN-g2fyi7Le_7xfPs,2828
@@ -157,19 +155,20 @@ 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=qS5Dsv7iKtXYc2WwNjex5dHpfvLy1cX6CukBVwc_zkM,18479
+biopipen/scripts/scrna/MarkersFinder.R,sha256=P6BgseCrXTeJR8X52hzD16qBUuCeHmPc96h5pKE_-qY,24207
 biopipen/scripts/scrna/MetaMarkers.R,sha256=BgYaWYEj6obwqaZaDWqNPtxb1IEEAnXAeBE0Ji9PvBA,12426
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=-tByCPk7i070LynAb0z2ANeRxr1QqiKP0dfrJm52jH4,4198
+biopipen/scripts/scrna/PseudoBulkDEG.R,sha256=32Hd3x2WyTFv175Os4bxf6goAcIq7QN8m1i7i7emnMI,22308
 biopipen/scripts/scrna/RadarPlots.R,sha256=Kn1E-hpczuujpgNjR8MqeIIVN-S3PbpmfcKWGKcNCVY,14546
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
 biopipen/scripts/scrna/SCP-plot.R,sha256=QcR2zOjRlSA_z4L8l89FWPU7TGxpXlKUe4kPdZU9MuY,787291
-biopipen/scripts/scrna/ScFGSEA.R,sha256=AQu_buJVoRFltclhh3NyJakggRyZMuKj9q_tgzMgNwE,8655
+biopipen/scripts/scrna/ScFGSEA.R,sha256=Cbr1RE4jD3CbR7K4Y1XWKfcqiqhZmzATCKEd3ysCnCc,11517
 biopipen/scripts/scrna/ScSimulation.R,sha256=q0-dXD9px1cApc_TxGmR-OdNHE8W1VSVWfSI57B96bo,1697
 biopipen/scripts/scrna/ScVelo.py,sha256=SPUZFgZW1Zhw-bnjJo98RK0vpuNFODQ8Q3eTguNc84k,21359
 biopipen/scripts/scrna/Seurat2AnnData.R,sha256=F8g5n2CqX4-KBggxd8ittz8TejYuqqNLMudAHdFt1QM,184
 biopipen/scripts/scrna/SeuratClusterStats-clustree.R,sha256=QmNJicjbLIXYg_RduXHGboCzPEqcFXq32flk5XAqQBg,2886
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=tCf3BVoXroeGuMcix8BiB1CA7wUpirBow4T6P3HM02k,1541
-biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=Ua4dCqekb2nmx9EEgiQamju4c0p96KWLJWAmiziwiec,5197
+biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=vFLTzF4hje-7JXy-hYxCZgsasbVByvVkqrTFlxzMTB0,5307
 biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=BN8HSl1HoZp8ibESaCVEJPCBWzmu1AFLMgW5ZeZphS0,3077
 biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=u8KOeWLDk7i-ZGGcgZPyNqmchkrePdKq5JLrl4ZCCT8,2297
 biopipen/scripts/scrna/SeuratClusterStats.R,sha256=lQfl97ARx_l8YNJ1rEdaU-G6EIS-mbFf2rtWLaA6unE,1824
@@ -185,7 +184,7 @@ biopipen/scripts/scrna/SeuratSubset.R,sha256=yVA11NVE2FSSw-DhxQcJRapns0tNNHdyDYi
 biopipen/scripts/scrna/SeuratTo10X.R,sha256=1mh1R0Qlo1iHVrpMLUXyLDOA92QKJ4GzTMURTFRqsWg,901
 biopipen/scripts/scrna/Slingshot.R,sha256=wo1zq2Wl6u1HODNzZGjjQLcqKeh9sh7FXPs_iKu6tqw,1750
 biopipen/scripts/scrna/Subset10X.R,sha256=dT1QY5mHaDcqOMgAtTfyU1FRBNFtfg3nMGCubvBJcSQ,2671
-biopipen/scripts/scrna/TopExpressingGenes.R,sha256=4z6BWnZdijN9aZaNjhwI04Vectzk01LqAYmvf_ksFag,6796
+biopipen/scripts/scrna/TopExpressingGenes.R,sha256=9xXx7U6ZLNeZslqhYuxWYQJmgUsTD3qXFew-7zYCJu8,6910
 biopipen/scripts/scrna/celltypist-wrapper.py,sha256=upyh035IqDHxljbTaoXwdDmctcx-fDwN56kGvC2xsbw,1776
 biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
 biopipen/scripts/scrna/seurat_anndata_conversion.py,sha256=Ya0Wn2TLg1j66N41PdiXXGE8LtE51eC8XnkGi_q2ey8,2437
@@ -214,7 +213,7 @@ biopipen/scripts/tcgamaf/MafAddChr.py,sha256=uo1utaK3Df88aU7xubKw85Ni7W06md8bQlw
 biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
 biopipen/scripts/tcr/Attach2Seurat.R,sha256=0KZaBkuPvqOBXq4ZG3pzIIua5HL-161K5dVXRoCysy4,1366
 biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=vU-5sjFZktSzBBj4f1frIGChOV8P8Uf0mMWS2Njdsww,15204
-biopipen/scripts/tcr/ClonalStats.R,sha256=89bow8pli4v26nZITPmcFT1cFkL4hZr-s8gxCod-X-0,29329
+biopipen/scripts/tcr/ClonalStats.R,sha256=skqPMTHL8zMGIZ2Q_gKXm9UDFRR-wFRurtrmvbQp7pg,29340
 biopipen/scripts/tcr/CloneResidency.R,sha256=3pong__cdn2bW7pctq4TLcEdcj_xNigzyKnznnmc1i8,22021
 biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=zw5WPgq_lbfdDb9Ou07boh9D2FYjXZtCQKZCP0PKMYw,4561
 biopipen/scripts/tcr/GIANA/GIANA.py,sha256=jo0d58K57CF4W6mc2Q-hQn9rLl6oLHTsr5JceP8xqN0,54874
@@ -236,7 +235,7 @@ biopipen/scripts/tcr/ImmunarchFilter.R,sha256=-en-zi0ZB1JjuqhPlaEAN8YvHrELZNJ1V7
 biopipen/scripts/tcr/ImmunarchLoading.R,sha256=u3o2aag_7cZ17HA8RxpN58wvrII0Uh-q6FY6dA8MWeQ,5756
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=oipN4-2nQZe8bYjI0lZ0SvZ7T8GZ_FWkpkobi1cwmWE,2664
-biopipen/scripts/tcr/ScRepCombiningExpression.R,sha256=IJ7wHFKL5STWPv-mtWWt1-Ly_Evei146U0y0ZB9jCGE,933
+biopipen/scripts/tcr/ScRepCombiningExpression.R,sha256=sPkCycfB0TrjqduFjZaeVG7MLi6RntXrihyjq5MDeDM,974
 biopipen/scripts/tcr/ScRepLoading.R,sha256=eqJXTXn_HyLRo98Hv6xI_AmYp5l2LxHsyrMSXWZ_HmM,5167
 biopipen/scripts/tcr/TCRClusterStats.R,sha256=ns3S95DVDBuhSe1YgTZ1OksbfBgREO2Tnp1d4QzbTw0,13530
 biopipen/scripts/tcr/TCRClustering.R,sha256=b-IZeE3Rcue4Ntn9H7FLljELzycbWCyKP17LlBCuMW0,9658
@@ -286,7 +285,7 @@ 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-0.34.0.dist-info/METADATA,sha256=s814Vi4vNzzMRB4tNOx-fEDPLHv1CiUHxN7Ls1GTyPc,975
-biopipen-0.34.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-biopipen-0.34.0.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.34.0.dist-info/RECORD,,
+biopipen-0.34.2.dist-info/METADATA,sha256=J4QZVcGfOyn69By9_QajoSA8UQvPzWFqsFaEwDvUv2I,975
+biopipen-0.34.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+biopipen-0.34.2.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.34.2.dist-info/RECORD,,

biopipen/reports/scrna/ScFGSEA.svelte

@@ -1,16 +0,0 @@
-{% from "utils/gsea.liq" import fgsea_report -%}
-{% from "utils/misc.liq" import report_jobs -%}
-<script>
-    import { Image, DataTable, Descr } from "$libs";
-    import { Accordion, AccordionItem, Tabs, Tab, TabContent, InlineNotification } from "$ccs";
-</script>
-
-{%- macro report_job(job, h=1) -%}
-    {{ job | render_job: h=h }}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-    <h1>{{job.in.srtobj | stem0 | escape}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/TopExpressingGenes.svelte

@@ -1,17 +0,0 @@
-{% from "utils/misc.liq" import report_jobs -%}
-{% from "utils/gsea.liq" import enrichr_report -%}
-<script>
-    import { Image, DataTable, Descr } from "$libs";
-    import { Accordion, AccordionItem, Tabs, Tab, TabContent, InlineNotification } from "$ccs";
-</script>
-
-
-{%- macro report_job(job, h=1) -%}
-    {{ job | render_job: h=h }}
-{%- endmacro -%}
-
-{%- macro head_job(job) -%}
-  <h1>{{job.in.srtobj | stem0 | escape}}</h1>
-{%- endmacro -%}
-
-{{ report_jobs(jobs, head_job, report_job) }}