biopipen 0.22.1__tar.gz → 0.22.2__tar.gz

{biopipen-0.22.1 → biopipen-0.22.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.22.1
+Version: 0.22.2
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.22.2/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.22.2"

{biopipen-0.22.1 → biopipen-0.22.2}/biopipen/core/config.toml

@@ -4,6 +4,8 @@
 bedtools = "bedtools"
 # bcftools to handle bcf/vcf files
 bcftools = "bcftools"
+# cellranger
+cellranger = "cellranger"
 # Control-FREEC to call cnvs
 freec = "freec"
 # liftover coordinates across genomes
@@ -59,6 +61,10 @@ liftover_chain = ""
 # tmpdir = ""
 
 [ref]
+# The reference for cellranger gex
+ref_cellranger_gex = ""
+# The reference for cellranger vdj
+ref_cellranger_vdj = ""
 # The reference genome
 reffa = ""
 # The directory with reference for each chromosome

{biopipen-0.22.1 → biopipen-0.22.2}/biopipen/core/filters.py

@@ -15,6 +15,7 @@ filtermanager = FilterManager()
 @filtermanager.register
 def dict_to_cli_args(
     dic: Mapping[str, Any],
+    exclude: List[str] = None,
     prefix: str | None = None,
     sep: str | None = " ",
     dup_key: bool = True,
@@ -27,6 +28,7 @@ def dict_to_cli_args(
 
     Args:
         dic: The dict to convert
+        exclude: The keys to exclude
         prefix: The prefix of the keys after conversion
             Defaults to `None`, mean `-` for short keys and `--` for long keys
         sep: The separator between key and value
@@ -37,6 +39,13 @@ def dict_to_cli_args(
             If `sep` is `None` or `=`, this must be True, otherwise an error
             will be raised
         join: Whether to join the arguments into a single string
+        start_key: The key to start the arguments
+            This is useful when you want to put some arguments at the beginning
+            of the command line
+        end_key: The key to end the arguments
+            This is useful when you want to put some arguments at the end
+            of the command line
+        dashify: Whether to replace `_` with `-` in the keys
 
     Returns:
         The converted string or list of strings
@@ -44,6 +53,9 @@ def dict_to_cli_args(
     if sep in [None, "="] and not dup_key:
         raise ValueError("`dup_key` must be True when sep is `None` or `=`")
 
+    if exclude:
+        dic = {k: v for k, v in dic.items() if k not in exclude}
+
     starts = []
     ends = []
     out = []

biopipen-0.22.2/biopipen/ns/cellranger.py

@@ -0,0 +1,101 @@
+"""Cellranger pipeline module for BioPipen"""
+from ..core.proc import Proc
+from ..core.config import config
+
+
+class CellRangerCount(Proc):
+    """Run cellranger count
+
+    to count gene expression and/or feature barcode reads
+
+    Input:
+        fastqs: The input fastq files
+            Either a list of fastq files or a directory containing fastq files
+            If a directory is provided, it should be passed as a list with one
+            element.
+
+    Output:
+        outdir: The output directory
+
+    Envs:
+        ncores: Number of cores to use
+        cellranger: Path to cellranger
+        ref: Path of folder containing 10x-compatible transcriptome reference
+        tmpdir: Path to temporary directory, used to save the soft-lined fastq files
+            to pass to cellranger
+        include_introns: Set to false to exclude intronic reads in count.
+        <more>: Other environment variables required by `cellranger count`
+            See `cellranger count --help` for more details or
+            https://www.10xgenomics.com/support/software/cell-ranger/advanced/cr-command-line-arguments#count
+    """  # noqa: E501
+    input = "fastqs:files"
+    output = """outdir:dir:
+        {%- set fastqs = in.fastqs -%}
+        {%- if len(fastqs) == 1 and isdir(fastqs[0]) -%}
+            {%- set fastqs = fastqs[0] | glob: "*.fastq.gz" -%}
+        {%- endif -%}
+        {%- set sample = commonprefix(*fastqs) |
+            regex_replace: "_L\\d+_$", "" |
+            regex_replace: "_S\\d+$", "" -%}
+        {{- sample -}}
+    """
+    lang = config.lang.python
+    envs = {
+        "ncores": config.misc.ncores,
+        "cellranger": config.exe.cellranger,
+        "ref": config.ref.ref_cellranger_gex,
+        "tmpdir": config.path.tmpdir,
+        "include_introns": "true",
+    }
+    script = "file://../scripts/cellranger/CellRangerCount.py"
+    plugin_opts = {
+        "report": "file://../reports/cellranger/CellRangerCount.svelte",
+    }
+
+
+class CellRangerVdj(Proc):
+    """Run cellranger vdj
+
+    to perform sequence assembly and paired clonotype calling
+
+    Input:
+        fastqs: The input fastq files
+            Either a list of fastq files or a directory containing fastq files
+            If a directory is provided, it should be passed as a list with one
+            element.
+
+    Output:
+        outdir: The output directory
+
+    Envs:
+        ncores: Number of cores to use
+        cellranger: Path to cellranger
+        ref: Path of folder containing 10x-compatible transcriptome reference
+        tmpdir: Path to temporary directory, used to save the soft-lined fastq files
+            to pass to cellranger
+        <more>: Other environment variables required by `cellranger vdj`
+            See `cellranger vdj --help` for more details or
+            https://www.10xgenomics.com/support/software/cell-ranger/advanced/cr-command-line-arguments#vdj
+    """  # noqa: E501
+    input = "fastqs:files"
+    output = """outdir:dir:
+        {%- set fastqs = in.fastqs -%}
+        {%- if len(fastqs) == 1 and isdir(fastqs[0]) -%}
+            {%- set fastqs = fastqs[0] | glob: "*.fastq.gz" -%}
+        {%- endif -%}
+        {%- set sample = commonprefix(*fastqs) |
+            regex_replace: "_L\\d+_$", "" |
+            regex_replace: "_S\\d+$", "" -%}
+        {{- sample -}}
+    """
+    lang = config.lang.python
+    envs = {
+        "ncores": config.misc.ncores,
+        "cellranger": config.exe.cellranger,
+        "ref": config.ref.ref_cellranger_vdj,
+        "tmpdir": config.path.tmpdir,
+    }
+    script = "file://../scripts/cellranger/CellRangerVdj.py"
+    plugin_opts = {
+        "report": "file://../reports/cellranger/CellRangerVdj.svelte",
+    }

{biopipen-0.22.1 → biopipen-0.22.2}/biopipen/ns/scrna.py

@@ -1422,6 +1422,8 @@ class CellTypeAnnotation(Proc):
             If the length of `cell_types` is shorter than the number of
             clusters, the remaining clusters will be kept as the original cell
             types.
+            You can also use `NA` to remove the clusters from downstream analysis. This
+            only works when `envs.newcol` is not specified.
 
             /// Note
             If `tool` is `direct` and `cell_types` is not specified or an empty list,

biopipen-0.22.2/biopipen/reports/cellranger/CellRangerCount.svelte

@@ -0,0 +1,16 @@
+{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+
+{%- macro report_job(job, h=1) -%}
+    <h{{h}}>{{job.out.outdir | basename | escape}}</h{{h}}>
+    <iframe
+        src="{{job.out.outdir}}/outs/web_summary.html"
+        width="100%"
+        frameborder="0"
+        style="min-height: 80vh"></iframe>
+{%- endmacro -%}
+
+{%- macro head_job(job) -%}
+    <h1>{{job.out.outdir | basename | escape}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen-0.22.2/biopipen/reports/cellranger/CellRangerVdj.svelte

@@ -0,0 +1,16 @@
+{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+
+{%- macro report_job(job, h=1) -%}
+    <h{{h}}>{{job.out.outdir | basename | escape}}</h{{h}}>
+    <iframe
+        src="{{job.out.outdir}}/outs/web_summary.html"
+        width="100%"
+        frameborder="0"
+        style="min-height: 80vh"></iframe>
+{%- endmacro -%}
+
+{%- macro head_job(job) -%}
+    <h1>{{job.out.outdir | basename | escape}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen-0.22.2/biopipen/scripts/cellranger/CellRangerCount.py

@@ -0,0 +1,79 @@
+import uuid
+import re
+from pathlib import Path
+from biopipen.utils.misc import run_command
+
+fastqs = {{in.fastqs | repr}}  # pyright: ignore  # noqa
+outdir = {{out.outdir | quote}}  # pyright: ignore
+
+cellranger = {{envs.cellranger | quote}}  # pyright: ignore
+tmpdir = Path({{envs.tmpdir | quote}})  # pyright: ignore
+ref = {{envs.ref | quote}}  # pyright: ignore
+ncores = {{envs.ncores | int}}  # pyright: ignore
+
+{% if "id" in envs -%}
+id = {{envs.id | quote}}  # pyright: ignore
+{%- else -%}
+id = {{out.outdir | basename | quote}}  # pyright: ignore
+{%- endif %}
+
+{% if "sample" in envs -%}
+sample = {{envs.sample | quote}}  # pyright: ignore
+{%- else -%}
+sample = {{out.outdir | basename | quote}}  # pyright: ignore
+{%- endif %}
+
+# create a temporary unique directory to store the soft-linked fastq files
+fastqdir = tmpdir / f"cellranger_count_{uuid.uuid4()}"
+fastqdir.mkdir(parents=True, exist_ok=True)
+if len(fastqs) == 1 and fastqs[0].is_dir():
+    fastqs = list(fastqs[0].glob("*.fastq.gz"))
+
+# soft-link the fastq files to the temporary directory
+for fastq in fastqs:
+    fastq = Path(fastq)
+    (fastqdir / fastq.name).symlink_to(fastq)
+
+other_args = {{envs | dict_to_cli_args: dashify=True, exclude=['cellranger', 'transcriptome', 'ref', 'tmpdir', 'id', 'sample', 'ncores']}}  # pyright: ignore
+
+command = [
+    cellranger,
+    "count",
+    "--id",
+    id,
+    "--sample",
+    sample,
+    "--fastqs",
+    fastqdir,
+    "--transcriptome",
+    ref,
+    "--localcores",
+    ncores,
+    "--disable-ui",
+    *other_args,
+]
+
+run_command(command, fg=True, cwd=str(Path(outdir).parent))
+
+web_summary_html = Path(outdir) / "outs" / "web_summary.html"
+if not web_summary_html.exists():
+    raise RuntimeError(
+        f"web_summary.html does not exist in {outdir}/outs. "
+        "cellranger count failed."
+    )
+
+# Modify web_summary.html to move javascript to a separate file
+# to void vscode live server breaking the page by injecting some code
+print("# Modify web_summary.html to move javascript to a separate file")
+try:
+    web_summary_js = Path(outdir) / "outs" / "web_summary.js"
+    web_summary_content = web_summary_html.read_text()
+    regex = re.compile(r"<script>(?=/\*! For license)(.+)</script>", re.DOTALL)
+    web_summary_html.write_text(regex.sub(
+        '<script src="web_summary.js"></script>',
+        web_summary_content,
+    ))
+    web_summary_js.write_text(regex.search(web_summary_content).group(1))
+except Exception as e:
+    print(f"Error modifying web_summary.html: {e}")
+    raise e

biopipen-0.22.2/biopipen/scripts/cellranger/CellRangerVdj.py

@@ -0,0 +1,79 @@
+import uuid
+import re
+from pathlib import Path
+from biopipen.utils.misc import run_command
+
+fastqs = {{in.fastqs | repr}}  # pyright: ignore  # noqa
+outdir = {{out.outdir | quote}}  # pyright: ignore
+
+cellranger = {{envs.cellranger | quote}}  # pyright: ignore
+tmpdir = Path({{envs.tmpdir | quote}})  # pyright: ignore
+ref = {{envs.ref | quote}}  # pyright: ignore
+ncores = {{envs.ncores | int}}  # pyright: ignore
+
+{% if "id" in envs -%}
+id = {{envs.id | quote}}  # pyright: ignore
+{%- else -%}
+id = {{out.outdir | basename | quote}}  # pyright: ignore
+{%- endif %}
+
+{% if "sample" in envs -%}
+sample = {{envs.sample | quote}}  # pyright: ignore
+{%- else -%}
+sample = {{out.outdir | basename | quote}}  # pyright: ignore
+{%- endif %}
+
+# create a temporary unique directory to store the soft-linked fastq files
+fastqdir = tmpdir / f"cellranger_count_{uuid.uuid4()}"
+fastqdir.mkdir(parents=True, exist_ok=True)
+if len(fastqs) == 1 and fastqs[0].is_dir():
+    fastqs = list(fastqs[0].glob("*.fastq.gz"))
+
+# soft-link the fastq files to the temporary directory
+for fastq in fastqs:
+    fastq = Path(fastq)
+    (fastqdir / fastq.name).symlink_to(fastq)
+
+other_args = {{envs | dict_to_cli_args: dashify=True, exclude=['cellranger', 'reference', 'ref', 'tmpdir', 'id', 'sample', 'ncores']}}  # pyright: ignore
+
+command = [
+    cellranger,
+    "vdj",
+    "--id",
+    id,
+    "--sample",
+    sample,
+    "--fastqs",
+    fastqdir,
+    "--reference",
+    ref,
+    "--localcores",
+    ncores,
+    "--disable-ui",
+    *other_args,
+]
+
+run_command(command, fg=True, cwd=str(Path(outdir).parent))
+
+web_summary_html = Path(outdir) / "outs" / "web_summary.html"
+if not web_summary_html.exists():
+    raise RuntimeError(
+        f"web_summary.html does not exist in {outdir}/outs. "
+        "cellranger vdj failed."
+    )
+
+# Modify web_summary.html to move javascript to a separate file
+# to void vscode live server breaking the page by injecting some code
+print("# Modify web_summary.html to move javascript to a separate file")
+try:
+    web_summary_js = Path(outdir) / "outs" / "web_summary.js"
+    web_summary_content = web_summary_html.read_text()
+    regex = re.compile(r"<script>(?=/\*! For license)(.+)</script>", re.DOTALL)
+    web_summary_html.write_text(regex.sub(
+        '<script src="web_summary.js"></script>',
+        web_summary_content,
+    ))
+    web_summary_js.write_text(regex.search(web_summary_content).group(1))
+except Exception as e:
+    print(f"Error modifying web_summary.html: {e}")
+    raise e

biopipen-0.22.2/biopipen/scripts/scrna/CellTypeAnnotation-direct.R

@@ -0,0 +1,55 @@
+source("{{biopipen_dir}}/utils/misc.R")
+library(Seurat)
+
+sobjfile <- {{in.sobjfile | r}}
+outfile <- {{out.outfile | r}}
+celltypes <- {{envs.cell_types | r}}
+newcol <- {{envs.newcol | r}}
+
+if (is.null(celltypes) || length(celltypes) == 0) {
+    log_warn("No cell types are given!")
+
+    # create a symbolic link to the input file
+    file.symlink(sobjfile, outfile)
+} else {
+    log_info("Loading Seurat object ...")
+    sobj <- readRDS(sobjfile)
+    idents <- as.character(unique(Idents(sobj)))
+    idents <- idents[order(as.numeric(idents))]
+
+    if (length(celltypes) < length(idents)) {
+        celltypes <- c(celltypes, idents[(length(celltypes) + 1):length(idents)])
+    } else if (length(celltypes) > length(idents)) {
+        celltypes <- celltypes[1:length(idents)]
+        log_warn("The length of cell types is longer than the number of clusters!")
+    }
+    for (i in seq_along(celltypes)) {
+        if (celltypes[i] == "-" || celltypes[i] == "") {
+            celltypes[i] <- idents[i]
+        }
+    }
+    names(celltypes) <- idents
+
+    log_info("Renaming cell types ...")
+    if (is.null(newcol)) {
+        has_na <- "NA" %in% unlist(celltypes) || anyNA(unlist(celltypes))
+        sobj$seurat_clusters_id <- Idents(sobj)
+        celltypes$object <- sobj
+        sobj <- do_call(RenameIdents, celltypes)
+        sobj$seurat_clusters <- Idents(sobj)
+        if (has_na) {
+            log_info("Filtering clusters if NA ...")
+            sobj <- subset(
+                sobj,
+                subset = seurat_clusters != "NA" & !is.na(seurat_clusters)
+            )
+        }
+    } else {
+        celltypes$object <- sobj
+        sobj <- do_call(RenameIdents, celltypes)
+        sobj[[newcol]] <- Idents(sobj)
+        Idents(sobj) <- "seurat_clusters"
+    }
+
+    saveRDS(sobj, outfile)
+}

{biopipen-0.22.1 → biopipen-0.22.2}/biopipen/scripts/scrna/CellsDistribution.R

@@ -142,13 +142,8 @@ do_case <- function(name, case) {
     info <- casename_info(name, create = TRUE)
     cells_by <- trimws(strsplit(case$cells_by, ",")[[1]])
 
-    sec_case_names <- strsplit(name, ":")[[1]]
-    sec_dir <- file.path(outdir, sec_case_names[1])
-    casename <- paste(sec_case_names[-1], collapse = ":")
-    dir.create(sec_dir, showWarnings = FALSE, recursive = TRUE)
-
-    outfile <- file.path(info$sec_dir, paste0("case-", info$case_slug, ".png"))
-    txtfile <- file.path(info$sec_dir, paste0("case-", info$case_slug, ".txt"))
+    outfile <- file.path(info$sec_dir, paste0(info$case_slug, ".png"))
+    txtfile <- file.path(info$sec_dir, paste0(info$case_slug, ".txt"))
 
     # subset the seurat object
     meta <- srtobj@meta.data
@@ -242,7 +237,7 @@ do_case <- function(name, case) {
         ),
         txtfile,
         sep = "\t",
-        row.names = TRUE,
+        row.names = FALSE,
         col.names = TRUE,
         quote = FALSE
     )

{biopipen-0.22.1 → biopipen-0.22.2}/biopipen/scripts/scrna/MarkersFinder.R

@@ -143,11 +143,13 @@ for (name in names(cases)) {
     } else if (is.null(case$each)) {
         # is.null(case$ident.1)
         sections <- c(sections, name)
-        idents <- srtobj@meta.data %>% pull(case$group.by) %>% unique() %>% na.omit()
-        for (ident in idents) {
-            newcases[[paste0(name, ":", ident)]] <- case
-            newcases[[paste0(name, ":", ident)]]$ident.1 <- ident
-        }
+        newcases[[name]] <- case
+        newcases[[name]]$findall <- TRUE
+        # idents <- srtobj@meta.data %>% pull(case$group.by) %>% unique() %>% na.omit()
+        # for (ident in idents) {
+        #     newcases[[paste0(name, ":", ident)]] <- case
+        #     newcases[[paste0(name, ":", ident)]]$ident.1 <- ident
+        # }
     } else {
         eachs <- srtobj@meta.data %>% pull(case$each) %>% unique() %>% na.omit()
         for (each in eachs) {
@@ -160,18 +162,22 @@ for (name in names(cases)) {
                 )
             )
             if (is.null(case$ident.1)) {
-                idents <- srtobj@meta.data %>% pull(case$group.by) %>% unique() %>% na.omit()
-                for (ident in idents) {
-                    kname <- if (name == "DEFAULT") "" else paste0(" - ", name)
-                    sections <- c(sections, paste0(each, kname))
-                    key <- paste0(each, kname, ":", ident)
-                    if (case$prefix_each) {
-                        key <- paste0(case$each, " - ", key)
-                    }
-                    newcases[[key]] <- case
-                    newcases[[key]]$ident.1 <- ident
-                    newcases[[key]]$group.by <- by
-                }
+                kname <- if (name == "DEFAULT") "" else paste0(" - ", name)
+                sections <- c(sections, paste0(each, kname))
+                key <- paste0(each, kname)
+                newcases[[key]] <- case
+                newcases[[key]]$group.by <- by
+                newcases[[key]]$findall <- TRUE
+                # idents <- srtobj@meta.data %>% pull(case$group.by) %>% unique() %>% na.omit()
+                # for (ident in idents) {
+                #     key <- paste0(each, kname, ":", ident)
+                #     if (case$prefix_each) {
+                #         key <- paste0(case$each, " - ", key)
+                #     }
+                #     newcases[[key]] <- case
+                #     newcases[[key]]$ident.1 <- ident
+                #     newcases[[key]]$group.by <- by
+                # }
             } else {
                 sections <- c(sections, case$each)
                 key <- paste0(case$each, ":", each)
@@ -312,11 +318,11 @@ do_enrich <- function(info, markers, sig, volgenes) {
 }
 
 
-do_dotplot <- function(info, siggenes, case, args) {
-    dotplot_devpars <- case$dotplot$devpars
+do_dotplot <- function(info, siggenes, dotplot, args) {
+    dotplot_devpars <- dotplot$devpars
     if (is.null(args$ident.2)) {
-        case$dotplot$object <- args$object
-        case$dotplot$object@meta.data <- case$dotplot$object@meta.data %>%
+        dotplot$object <- args$object
+        dotplot$object@meta.data <- dotplot$object@meta.data %>%
             mutate(
                 !!sym(args$group.by) := if_else(
                     !!sym(args$group.by) == args$ident.1,
@@ -329,17 +335,16 @@ do_dotplot <- function(info, siggenes, case, args) {
                 )
             )
     } else {
-        case$dotplot$object <- args$object %>%
+        dotplot$object <- args$object %>%
             filter(!!sym(args$group.by) %in% c(args$ident.1, args$ident.2)) %>%
             mutate(!!sym(args$group.by) := factor(
                 !!sym(args$group.by),
                 levels = c(args$ident.1, args$ident.2)
             ))
     }
-    case$dotplot$devpars <- NULL
-    case$dotplot$features <- siggenes
-    case$dotplot$group.by <- args$group.by
-    case$dotplot$assay <- case$assay
+    dotplot$devpars <- NULL
+    dotplot$features <- siggenes
+    dotplot$group.by <- args$group.by
     dotplot_width = ifelse(
         is.null(dotplot_devpars$width),
         if (length(siggenes) <= 20) length(siggenes) * 60 else length(siggenes) * 30,
@@ -351,7 +356,7 @@ do_dotplot <- function(info, siggenes, case, args) {
     png(dotplot_file, res = dotplot_res, width = dotplot_height, height = dotplot_width)
     # rotate x axis labels
     print(
-        do_call(DotPlot, case$dotplot) +
+        do_call(DotPlot, dotplot) +
         theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
         coord_flip()
     )
@@ -456,9 +461,79 @@ add_case_report <- function(info, sigmarkers, siggenes) {
 }
 
 
+do_case_findall <- function(casename) {
+    log_info("- Using FindAllMarkers for case: {casename}...")
+
+    case = cases[[casename]]
+    args <- case$rest
+    args$group.by <- case$group.by
+    if (is.null(args$logfc.threshold)) {
+        args$locfc.threshold <- 0
+    }
+    if (is.null(args$min.cells.group)) {
+        args$min.cells.group <- 1
+    }
+    if (is.null(args$min.cells.feature)) {
+        args$min.cells.feature <- 1
+    }
+    if (is.null(args$min.pct)) {
+        args$min.pct <- 0
+    }
+    if (!is.null(case$subset)) {
+        args$object <- srtobj %>% filter(!!parse_expr(case$subset) & filter(!is.na(!!sym(case$group.by))))
+    } else {
+        args$object <- srtobj %>% filter(!is.na(!!sym(case$group.by)))
+    }
+    Idents(args$object) <- case$group.by
+    markers <- tryCatch({
+        do_call(FindAllMarkers, args)
+        # gene, p_val, avg_log2FC, pct.1, pct.2, p_val_adj, cluster
+    }, error = function(e) {
+        log_warn(e$message)
+        data.frame(
+            gene = character(),
+            p_val = numeric(),
+            avg_log2FC = numeric(),
+            pct.1 = numeric(),
+            pct.2 = numeric(),
+            p_val_adj=numeric(),
+            cluster = character()
+        )
+    })
+
+    if (is.null(case$dotplot$assay)) {
+        case$dotplot$assay <- assay
+    }
+    idents <- unique(markers$cluster)
+    for (ident in idents) {
+        log_info("- Dealing with ident: {ident}...")
+        info <- casename_info(paste0(casename, ":", ident), create = TRUE)
+        siggenes <- do_enrich(info, markers %>% filter(cluster == ident), case$sigmarkers, case$volcano_genes)
+
+        if (length(siggenes) > 0) {
+            args$ident.1 <- as.character(ident)
+            do_dotplot(info, siggenes, case$dotplot, args)
+        }
+        add_case_report(info, case$sigmarkers, siggenes)
+
+        if (info$section %in% overlap) {
+            if (is.null(overlaps[[info$section]])) {
+                overlaps[[info$section]] <<- list()
+            }
+            overlaps[[info$section]][[info$case]] <<- siggenes
+        }
+    }
+}
+
+
 do_case <- function(casename) {
     log_info("Dealing with case: {casename}...")
 
+    if (isTRUE(cases[[casename]]$findall)) {
+        do_case_findall(casename)
+        return()
+    }
+
     info <- casename_info(casename, create = TRUE)
     case <- cases[[casename]]
     # ident1
@@ -507,7 +582,10 @@ do_case <- function(casename) {
     siggenes <- do_enrich(info, markers, case$sigmarkers, case$volcano_genes)
 
     if (length(siggenes) > 0) {
-        do_dotplot(info, siggenes, case, args)
+        if (is.null(case$dotplot$assay)) {
+            case$dotplot$assay <- assay
+        }
+        do_dotplot(info, siggenes, case$dotplot, args)
     }
 
     if (info$section %in% overlap) {

{biopipen-0.22.1 → biopipen-0.22.2}/biopipen/scripts/scrna/SeuratClusterStats-features.R

@@ -173,8 +173,8 @@ do_one_features = function(name) {
             rownames_to_column("Feature") %>%
             select(Feature, everything())
 
-        exprfile = paste0(slugify(name), ".txt")
-        write.table(expr, file.path(odir, exprfile), sep="\t", quote=FALSE, row.names=FALSE)
+        exprfile = file.path(odir, paste0(slugify(name), ".txt"))
+        write.table(expr, exprfile, sep="\t", quote=FALSE, row.names=FALSE)
 
         add_report(
             list(