biopipen 0.21.2__tar.gz → 0.22.1__tar.gz

{biopipen-0.21.2 → biopipen-0.22.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.21.2
+Version: 0.22.1
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.22.1/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.22.1"

{biopipen-0.21.2 → biopipen-0.22.1}/biopipen/core/filters.py

@@ -7,6 +7,7 @@ from typing import Any, List, Mapping
 
 from argx import Namespace
 from liquid.filters.manager import FilterManager
+from pipen_report.filters import register_component, render_ui, _tag
 
 filtermanager = FilterManager()
 
@@ -206,3 +207,144 @@ def r(
         return r(vars(obj), ignoreintkey, todot, sortkeys, skip, _i)
 
     return repr(obj)
+
+
+@register_component("fgsea")
+def _render_fgsea(
+    cont: Mapping[str, Any],
+    job: Mapping[str, Any],
+    level: int,
+    na_arg: str = "10",
+) -> str:
+    """Render fgsea report"""
+    # cont["dir"] is required
+    n_pathways = int(na_arg)
+    pathways = []
+    with Path(cont["dir"]).joinpath("fgsea.txt").open() as f:
+        next(f)  # skip header
+        for line in f:
+            pathway, _ = line.split("\t", 1)
+            pathways.append(pathway)
+            if len(pathways) >= n_pathways:
+                break
+
+    components = [
+        # Summary
+        {
+            "title": "Enrichment Analysis Summary",
+            "ui": "tabs",
+            "contents": [
+                {
+                    "title": "Plot",
+                    "ui": "flat",
+                    "contents": [
+                        {
+                            "kind": "image",
+                            "src": str(Path(cont["dir"]).joinpath("gsea_table.png")),
+                        }
+                    ],
+                },
+                {
+                    "title": "Table",
+                    "ui": "flat",
+                    "contents": [
+                        {
+                            "kind": "table",
+                            "src": str(Path(cont["dir"]).joinpath("fgsea.txt")),
+                        }
+                    ],
+                },
+            ]
+        },
+        # Pathways
+        {
+            "title": f"Enriched Pathways (Top {n_pathways})",
+            "ui": "table_of_images",
+            "contents": [
+                {
+                    "src": str(Path(cont["dir"]) / f"fgsea_{pw.replace('/', '-')}.png"),
+                    "title": pw,
+                }
+                for pw in pathways
+            ]
+        },
+    ]
+
+    return render_ui(components, "accordion", job, level)
+
+
+@register_component("pdf")
+def _render_pdf(
+    cont: Mapping[str, Any],
+    job: Mapping[str, Any],
+    level: int,
+) -> str:
+    """Render pdf report"""
+    # cont["src"] is required
+    height = cont.get("height", "600")
+    return _tag(
+        "embed",
+        src=str(cont["src"]),
+        type="application/pdf",
+        width="100%",
+        height=height,
+    )
+
+
+@register_component("gsea")
+def _render_gsea(
+    cont: Mapping[str, Any],
+    job: Mapping[str, Any],
+    level: int,
+) -> str:
+    """Render gsea report"""
+    # cont["dir"] is required
+    raise NotImplementedError()
+
+
+@register_component("enrichr")
+def _render_enrichr(
+    cont: Mapping[str, Any],
+    job: Mapping[str, Any],
+    level: int,
+) -> str:
+    """Render enrichr report"""
+    # cont["dir"] is required
+    dbs = [sumfile.stem[8:] for sumfile in Path(cont["dir"]).glob("Enrichr-*.txt")]
+    components = []
+
+    for db in dbs:
+        components.append(
+            {
+                "title": db,
+                "ui": "tabs",
+                "contents": [
+                    {
+                        "title": "Plot",
+                        "ui": "flat",
+                        "contents": [
+                            {
+                                "kind": "image",
+                                "src": str(
+                                    Path(cont["dir"]).joinpath(f"Enrichr-{db}.png")
+                                ),
+                            }
+                        ],
+                    },
+                    {
+                        "title": "Table",
+                        "ui": "flat",
+                        "contents": [
+                            {
+                                "kind": "table",
+                                "src": str(
+                                    Path(cont["dir"]).joinpath(f"Enrichr-{db}.txt")
+                                ),
+                            }
+                        ],
+                    },
+                ],
+            }
+        )
+
+    return render_ui(components, "accordion", job, level)

{biopipen-0.21.2 → biopipen-0.22.1}/biopipen/ns/scrna.py

@@ -257,6 +257,16 @@ class SeuratClustering(Proc):
             `object` is specified internally, and `-` in the key will be replaced with `.`.
             - resolution (type=float): The resolution of the clustering
             - <more>: See <https://satijalab.org/seurat/reference/findclusters>
+        cache (type=auto): Whether to cache the seurat object with cluster information.
+            If `True`, the seurat object will be cached in the job output directory, which will be not cleaned up when job is rerunning.
+            The cached seurat object will be saved as `<signature>.cached.RDS` file, where `<signature>` is the signature determined by
+            the input and envs of the process.
+            See <https://github.com/satijalab/seurat/issues/7849>, <https://github.com/satijalab/seurat/issues/5358> and
+            <https://github.com/satijalab/seurat/issues/6748> for more details.
+            To not use the cached seurat object, you can either set `cache` to `False` or delete the cached file at
+            `.pipen/<Pipeline>/SeuratClustering/0/output/<signature>.cached.RDS`.
+            You can also specify the directory to save the cached seurat object by setting `cache` to the directory path.
+
 
     Requires:
         r-seurat:
@@ -286,6 +296,7 @@ class SeuratClustering(Proc):
         "RunUMAP": {"reduction": "pca", "dims": 30},
         "FindNeighbors": {},
         "FindClusters": {"resolution": 0.8},
+        "cache": True,
     }
     script = "file://../scripts/scrna/SeuratClustering.R"
 
@@ -418,6 +429,7 @@ class SeuratClusterStats(Proc):
             - group-by: Same as `ident`. How the points are colored.
             - split-by: The column name in metadata to split the cells into different plots.
             - shape-by: The column name in metadata to use as the shape.
+            - subset: An expression to subset the cells, will be passed to `tidyrseurat::filter()`.
             - devpars (ns): The device parameters for the plots.
                 - res (type=int): The resolution of the plots.
                 - height (type=int): The height of the plots.
@@ -482,6 +494,7 @@ class SeuratClusterStats(Proc):
             "group-by": None,
             "split-by": None,
             "shape-by": None,
+            "subset": None,
             "reduction": "dim",
             "devpars": {"res": 100, "height": 800, "width": 1000},
         },
@@ -642,6 +655,7 @@ class CellsDistribution(Proc):
             Ignored if `cells_order` is specified.
         subset: An expression to subset the cells, will be passed to `dplyr::filter()` on metadata.
             This will be applied prior to `each`.
+        descr: The description of the case, will be shown in the report.
         devpars (ns): The device parameters for the plots.
             - res (type=int): The resolution of the plots
             - height (type=int): The height of the plots
@@ -676,6 +690,7 @@ class CellsDistribution(Proc):
         "cells_orderby": None,
         "cells_n": 10,
         "subset": None,
+        "descr": None,
         "devpars": {},
         "each": None,
         "section": "DEFAULT",
@@ -1669,7 +1684,7 @@ class RadarPlots(Proc):
         "cluster_order": [],
         "breaks": [],
         "direction": "intra-cluster",
-        "section": None,
+        "section": "DEFAULT",
         "devpars": {
             "res": 100,
             "width": 1200,
@@ -1719,6 +1734,8 @@ class MetaMarkers(Proc):
         dbs (list): The dbs to do enrichment analysis for significant
             markers See below for all libraries.
             <https://maayanlab.cloud/Enrichr/#libraries>
+        subset: The subset of the cells to do the analysis.
+            An expression passed to `dplyr::filter()`.
         p_adjust (choice): The method to adjust the p values, which can be used to filter the significant markers.
             See also <https://rdrr.io/r/stats/p.adjust.html>
             - holm: Holm-Bonferroni method
@@ -1759,6 +1776,7 @@ class MetaMarkers(Proc):
         "group-by": None,
         "idents": None,
         "each": None,
+        "subset": None,
         "prefix_each": True,
         "p_adjust": "BH",
         "dbs": [

{biopipen-0.21.2 → biopipen-0.22.1}/biopipen/ns/tcr.py

@@ -40,11 +40,13 @@ class ImmunarchLoading(Proc):
 
     Output:
         rdsfile: The RDS file with the data and metadata
-        metatxt: The meta data of the cells, used to attach to the Seurat object
+        metatxt: The meta data at cell level, which can be used to attach to the Seurat object
 
     Envs:
         prefix: The prefix to the barcodes. You can use placeholder like `{Sample}_`
-            to use the meta data from the `immunarch` object.
+            to use the meta data from the `immunarch` object. The prefixed barcodes will
+            be saved in `out.metatxt`. The `immunarch` object keeps the original barcodes, but
+            the prefix is saved at `immdata$prefix`.
 
             /// Note
             This option is useful because the barcodes for the cells from scRNA-seq
@@ -65,10 +67,16 @@ class ImmunarchLoading(Proc):
             paired chain data. For `single`, only TRB chain will be kept
             at `immdata$data`, information for other chains will be
             saved at `immdata$tra` and `immdata$multi`.
-        metacols (list): The columns to be exported to the text file.
+        extracols (list): The extra columns to be exported to the text file.
             You can refer to the
             [immunarch documentation](https://immunarch.com/articles/v2_data.html#immunarch-data-format)
-            for the full list of the columns.
+            to get a sense for the full list of the columns.
+            The columns may vary depending on the data source.
+            The columns from `immdata$meta` and some core columns, including
+            `Barcode`, `CDR3.aa`, `Clones`, `Proportion`, `V.name`, `J.name`, and
+            `D.name` will be exported by default. You can use this option to
+            specify the extra columns to be exported.
+
     """  # noqa: E501
     input = "metafile:file"
     output = [
@@ -80,7 +88,7 @@ class ImmunarchLoading(Proc):
         "tmpdir": config.path.tmpdir,
         "prefix": "{Sample}_",
         "mode": "single",
-        "metacols": ["Clones", "Proportion", "CDR3.aa"],
+        "extracols": [],
     }
     script = "file://../scripts/tcr/ImmunarchLoading.R"
 
@@ -322,6 +330,7 @@ class Immunarch(Proc):
         prefix: The prefix to the barcodes. You can use placeholder like `{Sample}_`
             The prefixed barcodes will be used to match the barcodes in `in.metafile`.
             Not used if `in.metafile` is not specified.
+            If `None` (default), `immdata$prefix` will be used.
         volumes (ns): Explore clonotype volume (sizes).
             - by: Groupings when visualize clonotype volumes, passed to the `.by` argument of `vis(imm_vol, .by = <values>)`.
                 Multiple columns should be separated by `,`.
@@ -682,7 +691,7 @@ class Immunarch(Proc):
     lang = config.lang.rscript
     envs = {
         "mutaters": {},
-        "prefix": "{Sample}_",
+        "prefix": None,
         # basic statistics
         "volumes": {
             "by": None,
@@ -1179,6 +1188,10 @@ class TCRClustering(Proc):
             For GIANA, using TRBV mutations is not supported
             - GIANA: by Li lab at UT Southwestern Medical Center
             - ClusTCR: by Sebastiaan Valkiers, etc
+        prefix: The prefix to the barcodes. You can use placeholder like `{Sample}_`
+            The prefixed barcodes will be used to match the barcodes in `in.metafile`.
+            Not used if `in.metafile` is not specified.
+            If `None` (default), `immdata$prefix` will be used.
         python: The path of python with `GIANA`'s dependencies installed
             or with `clusTCR` installed. Depending on the `tool` you choose.
         args (type=json): The arguments for the clustering tool
@@ -1202,6 +1215,7 @@ class TCRClustering(Proc):
     lang = config.lang.rscript
     envs = {
         "tool": "GIANA",  # or ClusTCR
+        "prefix": None,
         "on_multi": False,
         "python": config.lang.python,
         "args": {},
@@ -1507,7 +1521,8 @@ class TESSA(Proc):
             [link](https://www.nature.com/articles/s42256-021-00383-2)
 
     Input:
-        immdata: The data loaded by `immunarch::repLoad()`, saved in RDS format
+        immdata: The immunarch object in RDS file or text file of TCR data loaded by
+            [`ImmunarchLoading`](!!#biopipennstcrimmunarchloading)
         srtobj: The `Seurat` object, saved in RDS format, with dimension
             reduction performed if you want to use them to represent the
             transcriptome of T cells.
@@ -1522,8 +1537,13 @@ class TESSA(Proc):
 
     Envs:
         python: The path of python with `TESSA`'s dependencies installed
-        prefix: The prefix to the barcodes of TCR data. You can use placeholder
-            like `{Sample}_` to use the meta data from the immunarch object.
+        prefix: The prefix of the cell barcodes in the `Seurat` object.
+            Once could use a fixed prefix, or a placeholder with the column
+            name in meta data. For example, `"{Sample}_"` will replace the
+            placeholder with the value of the column `Sample` in meta data.
+            If `in.immdata` is text file, the prefix will be ignored and the
+            barcode should be already prefixed.
+            If `None` and `in.immdata` is RDS file, `immdata$prefix` will be used.
         within_sample (flag): Whether the TCR networks are constructed only
             within TCRs from the same sample/patient (True) or with all the
             TCRs in the meta data matrix (False).
@@ -1548,7 +1568,7 @@ class TESSA(Proc):
     lang = config.lang.rscript
     envs = {
         "python": config.lang.python,
-        "prefix": "{Sample}_",
+        "prefix": None,
         "assay": "RNA",
         "within_sample": False,
         "predefined_b": False,

biopipen-0.22.1/biopipen/reports/delim/SampleInfo.svelte

@@ -0,0 +1,16 @@
+{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+
+<script>
+    import { Image, DataTable, Descr } from "$libs";
+</script>
+
+{%- macro report_job(job, h=1) -%}
+    {{ job | render_job: h=h }}
+{%- endmacro -%}
+
+{%- macro head_job(job) -%}
+    <h1>{{job.in.infile | stem | escape }}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}
+

biopipen-0.22.1/biopipen/reports/scrna/CellsDistribution.svelte

@@ -0,0 +1,15 @@
+{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+<script>
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent } from "$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-0.22.1/biopipen/reports/scrna/MarkersFinder.svelte

@@ -0,0 +1,18 @@
+{% from "utils/misc.liq" import report_jobs -%}
+
+<script>
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent, InlineNotification, Accordion, AccordionItem } from "$ccs";
+</script>
+
+
+{%- macro report_job(job, h=1) -%}
+    {{ job | render_job: h=h }}
+{%- endmacro -%}
+
+
+{%- macro head_job(job) -%}
+    <h1>{{job.in.srtobj | stem | escape}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen-0.22.1/biopipen/reports/scrna/MetaMarkers.svelte

@@ -0,0 +1,18 @@
+{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+{% from "utils/gsea.liq" import enrichr_report -%}
+<script>
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent, InlineNotification, Accordion, AccordionItem } from "$ccs";
+</script>
+
+
+{%- macro report_job(job, h=1) -%}
+    {{ job | render_job: h=h }}
+{%- endmacro -%}
+
+
+{%- macro head_job(job) -%}
+  <h1>{{job.in.srtobj | stem | escape}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen-0.22.1/biopipen/reports/scrna/RadarPlots.svelte

@@ -0,0 +1,15 @@
+{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+<script>
+    import { Image, DataTable } from "$libs";
+    import { Tabs, Tab, TabContent } from "$ccs";
+</script>
+
+{%- macro report_job(job, h=1) -%}
+    {{ job | render_job: h=h }}
+{%- endmacro -%}
+
+{%- macro head_job(job) -%}
+    <h1>{{job.in.srtobj | stem}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen-0.22.1/biopipen/reports/scrna/ScFGSEA.svelte

@@ -0,0 +1,16 @@
+{% from "utils/gsea.liq" import fgsea_report -%}
+{% from "utils/misc.liq" import report_jobs -%}
+<script>
+    import { Image, DataTable, Descr } from "$libs";
+    import { Accordion, AccordionItem, Tabs, Tab, TabContent } from "$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-0.22.1/biopipen/reports/scrna/SeuratClusterStats.svelte

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

biopipen-0.22.1/biopipen/reports/scrna/SeuratPreparing.svelte

@@ -0,0 +1,15 @@
+{% from "utils/misc.liq" import report_jobs -%}
+{% from_ os import path %}
+<script>
+    import { Image, DataTable, Descr } from "$libs";
+</script>
+
+{%- macro report_job(job, h=1) -%}
+    {{ job | render_job: h=h }}
+{%- endmacro -%}
+
+{%- macro head_job(job) -%}
+    <h1>{{job.in.metafile | stem}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen-0.22.1/biopipen/reports/scrna/TopExpressingGenes.svelte

@@ -0,0 +1,17 @@
+{% from "utils/misc.liq" import report_jobs -%}
+{% from "utils/gsea.liq" import enrichr_report -%}
+<script>
+    import { Image, DataTable, Descr } from "$libs";
+    import { Accordion, AccordionItem, Tabs, Tab, TabContent } from "$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-0.22.1/biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte

@@ -0,0 +1,32 @@
+{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+{% from "utils/gsea.liq" import fgsea_report_script, fgsea_report, gsea_report -%}
+
+<script>
+  import { Image, DataTable, Descr } from "$libs";
+  import { Tabs, Tab, TabContent, Accordion, AccordionItem } from "$ccs";
+</script>
+
+{%- macro report_job(job, h=2) -%}
+  {% if envs.fgsea %}
+    {{ job | render_job: h=h }}
+  {% else %}
+    {%- for ssdir in job.out.outdir | glob: "*" -%}
+      {%- if basename(ssdir) == "ALL" -%}
+        {%- set h = 1 -%}
+      {%- else -%}
+        <h{{h}}>{{ ssdir | stem }}</h{{h}}>
+      {%- endif -%}
+
+      {% for cldir in ssdir | glob: '*' %}
+        <h{{h+1}}>{{ cldir | basename }}</h{{h+1}}>
+        {{ gsea_report(cldir, h+2, envs, envs.top) }}
+      {% endfor %}
+    {%- endfor -%}
+  {% endif %}
+{%- endmacro -%}
+
+{%- macro head_job(job) -%}
+  <h1>{{job.in.sobjfile | stem | escape}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen-0.22.1/biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.svelte

@@ -0,0 +1,28 @@
+{% from "utils/misc.liq" import report_jobs, table_of_images -%}
+{% from "utils/gsea.liq" import fgsea_report, gsea_report -%}
+
+<script>
+  import { Image, DataTable, Descr } from "$libs";
+  import { Tabs, Tab, TabContent, Accordion, AccordionItem } from "$ccs";
+</script>
+
+{%- macro report_job(job, h=2) -%}
+  {% if envs.fgsea %}
+    {{ job | render_job: h=h }}
+  {% else %}
+    {%  for groupdir in job.out.outdir | glob: "*" %}
+      <h{{h}}>{{groupdir | basename}}</h{{h}}>
+      {%- set dsdirs = groupdir | glob: "*" -%}
+      {% for dsdir in groupdir | glob: "*" %}
+          <h{{h+1}}>{{ dsdir | basename }}</h{{h+1}}>
+          {{ gsea_report(dsdir, h+2, envs, envs.top) }}
+      {% endfor %}
+    {% endfor %}
+  {% endif %}
+{%- endmacro -%}
+
+{%- macro head_job(job) -%}
+  <h1>{{job.in.sobjfile | stem | escape}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen-0.22.1/biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte

@@ -0,0 +1,89 @@
+{% from "utils/misc.liq" import report_jobs -%}
+
+<script>
+    import { Image, Descr } from "$libs";
+    import { ListItem, UnorderedList } from "$ccs";
+</script>
+
+<h1>Introduction</h1>
+
+<Descr>
+    Metabolic landscape of single cells in the tumor microenvironment.
+</Descr>
+
+<h2>Workflow of the original analysis</h2>
+<Image src="https://github.com/LocasaleLab/Single-Cell-Metabolic-Landscape/raw/master/pipeline.png" />
+
+<h2>Reference</h2>
+<UnorderedList>
+    <ListItem><a href="https://www.nature.com/articles/s41467-019-11738-0" target="_blank">
+        Zhengtao, Ziwei Dai, and Jason W. Locasale.
+        "Metabolic landscape of the tumor microenvironment at single cell resolution."
+        Nature communications 10.1 (2019): 1-12.
+    </a></ListItem>
+    <ListItem><a href="https://github.com/LocasaleLab/Single-Cell-Metabolic-Landscape" target="_blank">
+        Orginal pipeline
+    </a></ListItem>
+</UnorderedList>
+
+<h2>Analyses with this pipeline</h2>
+
+<Descr>
+The cells are grouped at 2 dimensions: `grouping`, usually the cell types, and `subsetting`, usually
+the groups that bring biological meaning (i.e. different timepoints or sample types (tumor/normal)).
+</Descr>
+
+<UnorderedList>
+<ListItem>
+    MetabolicPathwayActivity (this page)
+    <p>Investigating the metabolic pathways of the cells in different groups and subsets.</p>
+    <p>The cells are first grouped by subsets and then the metabolic activities are examined for each groups in different subsets.</p>
+</ListItem>
+<ListItem>
+    <a href="../MetabolicPathwayHeterogeneity/index.html">MetabolicPathwayHeterogeneity</a>
+    <p>Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</p>
+</ListItem>
+<ListItem>
+    <a href="../MetabolicFeatures/index.html">MetabolicFeatures</a>
+    <p>Gene set enrichment analysis against the metabolic pathways for groups in different subsets.</p>
+</ListItem>
+<ListItem>
+    <a href="../MetabolicFeaturesIntraSubsets/index.html">MetabolicFeaturesIntraSubsets</a>
+    <p>Gene set enrichment analysis against the metabolic pathways for subsets in different groups.</p>
+</ListItem>
+</UnorderedList>
+
+
+{%- macro report_job(job, h=2) -%}
+  {%- for ssdir in job.out.outdir | glob: "*" -%}
+  {%- if not isdir(ssdir) -%}
+    {%- continue -%}
+  {%- endif -%}
+  <h{{h}}>{{ ssdir | stem }}</h{{h}}>
+
+  <h{{ h+1 }}>Metabolic pathway activities by <code>{{envs.grouping}}</code></h{{ h+1 }}>
+  <Image src="{{ssdir | joinpaths: 'KEGGpathway_activity_heatmap.png'}}" />
+
+  <h{{ h+1 }}>Distributions of pathway activities by <code>{{envs.grouping}}</code></h{{ h+1 }}>
+  <Image src="{{ssdir | joinpaths: 'pathway_activity_violinplot.png'}}" />
+  {%- endfor -%}
+
+  {% if job.out.outdir | glob: "*.group-*.png" -%}
+  <h{{h}}>Merged heatmaps</h{{h}}>
+  {% for group_hm in job.out.outdir | glob: "*.group-*.png" -%}
+    {%- if group_hm.endswith(".group-unclustered.png") -%}
+        <h{{h+1}}>{{group_hm | stem | replace: ".group-unclustered", " (Group Unclustered)"}}</h{{h+1}}>
+        <Image src="{{group_hm}}" />
+    {%- else -%}
+        <h{{h+1}}>{{group_hm | stem | replace: ".group-clustered", " (Group Clustered)"}}</h{{h+1}}>
+        <Image src="{{group_hm}}" />
+    {%- endif -%}
+  {%- endfor -%}
+  {%- endif -%}
+{%- endmacro -%}
+
+{%- macro head_job(job) -%}
+  <h1>{{job.in.sobjfile | stem | escape}}</h1>
+{%- endmacro -%}
+
+{{ report_jobs(jobs, head_job, report_job) }}