biopipen 0.21.0__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/reports/scrna/MarkersFinder.svelte

@@ -1,138 +1,18 @@
 {% from "utils/misc.liq" import report_jobs -%}
-{% from "utils/gsea.liq" import enrichr_report -%}
+
 <script>
-    import { Image, DataTable } from "$libs";
-    import { Tabs, Tab, TabContent, InlineNotification } from "$ccs";
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent, InlineNotification, Accordion, AccordionItem } from "$ccs";
 </script>
 
 
 {%- macro report_job(job, h=1) -%}
-    {%- set alldirs = job.out.outdir | glob: "*" -%}
-    {%- set ovdir = job.out.outdir | joinpaths: "OVERLAPS" -%}
-    {%- set secdirs = [] -%}
-    {%- for adir in alldirs -%}
-        {%- if basename(adir) != "OVERLAPS" -%}
-            {%- set _ = secdirs.append(adir) -%}
-        {%- endif -%}
-    {%- endfor -%}
-
-    {%- if len(secdirs) == 1 -%}
-        {%- set secname = secdirs | first | basename -%}
-        {%- for casedir in secdirs[0] | glob: "*" -%}
-            {%- if secname == "DEFAULT" -%}
-                <h{{h}}>{{casedir | basename | escape}}</h{{h}}>
-            {%- else -%}
-                <h{{h}}>{{secname | escape}} - {{casedir | basename | escape}}</h{{h}}>
-            {%- endif -%}
-            {%- if casedir | joinpaths: "error.txt" | exists -%}
-                <InlineNotification
-                    hideCloseButton
-                    lowContrast
-                    kind="warning"
-                    subtitle={{ casedir | joinpaths: "error.txt" | read | quote }}
-                    />
-            {%- else -%}
-                <h{{h+1}}>Markers</h{{h+1}}>
-                <Tabs>
-                    <Tab label="Markers" />
-                    <Tab label="Volcano Plot" />
-                    <Tab label="Dot Plot" />
-                    <svelte:fragment slot="content">
-                        <TabContent>
-                            <DataTable
-                                src={{ casedir | joinpaths: "markers.txt" | quote }}
-                                data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                                />
-                        </TabContent>
-                        <TabContent>
-                            <Image src={{ casedir | joinpaths: "volcano.png" | quote }} />
-                        </TabContent>
-                        <TabContent>
-                            <Image src={{ casedir | joinpaths: "dotplot.png" | quote }} />
-                        </TabContent>
-                    </svelte:fragment>
-                </Tabs>
-
-                <h{{h+1}}>Enrichment analysis</h{{h+1}}>
-                {{ enrichr_report(casedir) }}
-            {%- endif -%}
-        {%- endfor -%}
-    {%- else -%}
-        {%- for secdir in secdirs -%}
-            {%- set sec = secdir | basename -%}
-            <h{{h}}>{{sec | escape}}</h{{h}}>
-            {%- for casedir in secdir | glob: "*" -%}
-                <h{{h+1}}>{{casedir | basename | escape}}</h{{h+1}}>
-                {%- if casedir | joinpaths: "error.txt" | exists -%}
-                    <InlineNotification
-                        hideCloseButton
-                        lowContrast
-                        kind="warning"
-                        subtitle={{ casedir | joinpaths: "error.txt" | read | quote }}
-                        />
-                {%- else -%}
-                    <h{{h+2}}>Markers</h{{h+2}}>
-                    <Tabs>
-                        <Tab label="Markers" />
-                        <Tab label="Volcano Plot" />
-                        <Tab label="Dot Plot" />
-                        <svelte:fragment slot="content">
-                            <TabContent>
-                                <DataTable
-                                    src={{ casedir | joinpaths: "markers.txt" | quote }}
-                                    data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                                    />
-                            </TabContent>
-                            <TabContent>
-                                <Image src={{ casedir | joinpaths: "volcano.png" | quote }} />
-                            </TabContent>
-                            <TabContent>
-                                <Image src={{ casedir | joinpaths: "dotplot.png" | quote }} />
-                            </TabContent>
-                        </svelte:fragment>
-                    </Tabs>
-
-                    <h{{h+2}}>Enrichment analysis</h{{h+2}}>
-                    {{ enrichr_report(casedir) }}
-                {%- endif -%}
-            {%- endfor -%}
-        {%- endfor -%}
-    {%- endif -%}
-
-    {%- if ovdir | exists -%}
-        <h{{h}}>Overlapping Markers</h{{h}}>
-        {%- for casedir in ovdir | glob: "*" -%}
-            <h{{h+1}}>{{casedir | basename | escape}}</h{{h+1}}>
-            <Tabs>
-                {%- if casedir | joinpaths: "venn.png" | exists -%}
-                <Tab label="Venn Diagram" />
-                {%- endif -%}
-                <Tab label="UpSet Plot" />
-                <Tab label="Marks" />
-                <svelte:fragment slot="content">
-                    {%- if casedir | joinpaths: "venn.png" | exists -%}
-                    <TabContent>
-                        <Image src={{ casedir | joinpaths: "venn.png" | quote }} />
-                    </TabContent>
-                    {%- endif -%}
-                    <TabContent>
-                        <Image src={{ casedir | joinpaths: "upset.png" | quote }} />
-                    </TabContent>
-                    <TabContent>
-                        <DataTable
-                            src={{ casedir | joinpaths: "markers.txt" | quote }}
-                            data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t" }} }
-                            />
-                    </TabContent>
-                </svelte:fragment>
-            </Tabs>
-        {%- endfor -%}
-    {%- endif -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 
 {%- macro head_job(job) -%}
-  <h1>{{job.in.srtobj | stem | escape}}</h1>
+    <h1>{{job.in.srtobj | stem | escape}}</h1>
 {%- endmacro -%}
 
-{{ report_jobs(jobs, head_job, report_job) }}
+{{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna/MetaMarkers.svelte

@@ -1,85 +1,13 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 {% from "utils/gsea.liq" import enrichr_report -%}
 <script>
-    import { Image, DataTable } from "$libs";
-    import { Tabs, Tab, TabContent, InlineNotification } from "$ccs";
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent, InlineNotification, Accordion, AccordionItem } from "$ccs";
 </script>
 
 
 {%- macro report_job(job, h=1) -%}
-    {%- set secdirs = job.out.outdir | glob: "*" -%}
-    {%- if len(secdirs) == 1 -%}
-        {%- set secname = secdirs | first | basename -%}
-        {%- for casedir in secdirs[0] | glob: "*" -%}
-            {%- if secname == "DEFAULT" -%}
-                <h{{h}}>{{casedir | basename | escape}}</h{{h}}>
-            {%- else -%}
-                <h{{h}}>{{secname | escape}} - {{casedir | basename | escape}}</h{{h}}>
-            {%- endif -%}
-            {%- if casedir | joinpaths: "error.txt" | exists -%}
-                <InlineNotification
-                    hideCloseButton
-                    lowContrast
-                    kind="warning"
-                    subtitle={{ casedir | joinpaths: "error.txt" | read | quote }}
-                    />
-            {%- else -%}
-                <h{{h+1}}>Markers</h{{h+1}}>
-                <Tabs>
-                    <Tab label="Top 10 genes" />
-                    <Tab label="Table of top 100 genes" />
-                    <div slot="content">
-                    <TabContent>
-                        {{ table_of_images(glob(casedir, "plots", "*.png"), col = 4) }}
-                    </TabContent>
-                    <TabContent>
-                        <DataTable
-                            src={{ casedir | joinpaths: "markers.txt" | quote }}
-                            data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                            />
-                    </TabContent>
-                    </div>
-                </Tabs>
-
-                <h{{h+1}}>Enrichment analysis</h{{h+1}}>
-                {{ enrichr_report(casedir) }}
-            {%- endif -%}
-        {%- endfor -%}
-    {%- else -%}
-        {%- for secdir in secdirs -%}
-            {%- set sec = secdir | basename -%}
-            <h{{h}}>{{sec | escape}}</h{{h}}>
-            {%- for casedir in secdir | glob: "*" -%}
-                <h{{h+1}}>{{casedir | basename | escape}}</h{{h+1}}>
-                {%- if casedir | joinpaths: "error.txt" | exists -%}
-                    <InlineNotification
-                        hideCloseButton
-                        lowContrast
-                        kind="warning"
-                        subtitle={{ casedir | joinpaths: "error.txt" | read | quote }}
-                        />
-                {%- else -%}
-                    <h{{h+2}}>Markers</h{{h+2}}>
-                    <Tabs>
-                        <Tab label="Top 10 genes" />
-                        <Tab label="Table of top 100 genes" />
-                        <TabContent>
-                            {{ table_of_images(glob(casedir, "plots", "*.png"), col = 4) }}
-                        </TabContent>
-                        <TabContent>
-                            <DataTable
-                                src={{ casedir | joinpaths: "markers.txt" | quote }}
-                                data={ {{ casedir | joinpaths: "markers.txt" | datatable: sep="\t", nrows=100 }} }
-                                />
-                        </TabContent>
-                    </Tabs>
-
-                    <h{{h+2}}>Enrichment analysis</h{{h+2}}>
-                    {{ enrichr_report(casedir) }}
-                {%- endif -%}
-            {%- endfor -%}
-        {%- endfor -%}
-    {%- endif -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 

biopipen/reports/scrna/RadarPlots.svelte

@@ -1,31 +1,15 @@
 {% from "utils/misc.liq" import report_jobs, table_of_images -%}
 <script>
-    import { Image } from "$libs";
+    import { Image, DataTable } from "$libs";
+    import { Tabs, Tab, TabContent } from "$ccs";
 </script>
 
 {%- macro report_job(job, h=1) -%}
-    {%- set section_file = job.out.outdir | joinpaths: "sections.toml" -%}
-    {%- if section_file | exists -%}
-        {%- set sections = section_file | config: "toml" -%}
-        {%- for section, cases in sections.items() -%}
-            <h{{h}}>{{section | escape}}</h{{h}}>
-            {%- set imgs = [] -%}
-            {%- for case in cases -%}
-                {%- set img = job.out.outdir | joinpaths: case + ".png" -%}
-                {%- set _ = imgs.append(img) -%}
-            {%- endfor -%}
-            {{ table_of_images(imgs) }}
-        {%- endfor -%}
-    {%- else -%}
-        {%- for img in job.out.outdir | glob: "*.png" -%}
-            <h{{h}}>{{img | stem | escape}}</h{{h}}>
-            <Image src={{img | quote}} />
-        {%- endfor -%}
-    {%- endif -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}
-<h1>{{job.in.srtobj | stem}}</h1>
+    <h1>{{job.in.srtobj | stem}}</h1>
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte

@@ -1,31 +1,70 @@
-{% from "utils/misc.liq" import report_jobs, table_of_images -%}
-{% from "utils/gsea.liq" import fgsea_report_script, fgsea_report, gsea_report -%}
-
+{% from "utils/misc.liq" import report_jobs -%}
 <script>
-{{ fgsea_report_script() }}
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent, UnorderedList, ListItem, InlineNotification, Tile } from "$ccs";
 </script>
 
-{%- macro report_job(job, h=2) -%}
-  {%- 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}}>
-      {% if envs.fgsea %}
-          {{ fgsea_report(cldir, h+2, envs, envs.top) }}
-      {% else %}
-          {{ gsea_report(cldir, h+2, envs, envs.top) }}
-      {% endif %}
-    {% endfor %}
-  {%- endfor -%}
+<h1>Introduction</h1>
+
+<Descr>
+    Metabolic landscape of single cells in the tumor microenvironment.
+</Descr>
+
+<h2>Workflow of the original analysis</h2>
+<Image src="https://raw.githubusercontent.com/LocasaleLab/Single-Cell-Metabolic-Landscape/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: `subset_by`, usually the clinic groups that bring biological meaning
+(i.e. different timepoints or sample types (tumor/normal)), and `group_by`, usually the cell types.
+</Descr>
+
+<UnorderedList>
+<ListItem>
+    <a href="?proc=MetabolicPathwayActivity" class="listitem">MetabolicPathwayActivity</a>
+    <Tile><p>Investigating the metabolic pathways of the cells in different subsets and groups.</p></Tile>
+</ListItem>
+<ListItem>
+    <a href="?proc=MetabolicPathwayHeterogeneity" class="listitem">MetabolicPathwayHeterogeneity</a>
+    <Tile><p>Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</p></Tile>
+</ListItem>
+<ListItem>
+    <span class="listitem">MetabolicFeatures (this page)</span>
+    <Tile>
+    <p>Gene set enrichment analysis against the metabolic pathways for comparisons by different groups in different subsets.</p>
+    <p>The metabolic features are actual gene set enrichment analysis (GSEA) results for the metabolic pathways with given comparisons.</p>
+    </Tile>
+</ListItem>
+</UnorderedList>
+
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>
+
+{%- macro report_job(job, h=1) -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}
-  <h1>{{job.in.sobjfile | stem | escape}}</h1>
+    <h1>{{job.in | attr: "values" | call | first | stem0 | escape}}</h1>
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte

@@ -1,97 +1,103 @@
 {% from "utils/misc.liq" import report_jobs -%}
-
 <script>
-    import { Image } from "$libs";
+    import { Image, DataTable, Descr, Math } from "$libs";
+    import { Tabs, Tab, TabContent, UnorderedList, ListItem, InlineNotification, Tile } from "$ccs";
 </script>
 
 <h1>Introduction</h1>
 
-<div class="markdown-wrap">
-<Markdown>
-
-Metabolic landscape of single cells in the tumor microenvironment.
-
-## Workflow of the original analysis
-<Image src="https://github.com/LocasaleLab/Single-Cell-Metabolic-Landscape/raw/master/pipeline.png" />
-
-## Reference
-- [Xiao, Zhengtao, Ziwei Dai, and Jason W. Locasale. "Metabolic landscape of the tumor microenvironment at single cell resolution." Nature communications 10.1 (2019): 1-12.](https://www.nature.com/articles/s41467-019-11738-0)
-- [Original pipeline](https://github.com/LocasaleLab/Single-Cell-Metabolic-Landscape)
-
-## Analyses with this pipeline
-
-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)).
-
-- **MetabolicPathwayActivity (this page)**
-
-    Investigating the metabolic pathways of the cells in different groups and subsets.
-
-    The cells are first grouped by subsets and then the metabolic activities are examined for each groups in different subsets.
-
-- **MetabolicPathwayHeterogeneity**
-
-    Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities
-
-- **MetabolicFeatures**
-
-    Gene set enrichment analysis against the metabolic pathways for groups in different subsets.
-
-- **MetabolicFeaturesIntraSubsets** (optional)
-
-    Gene set enrichment analysis against the metabolic pathways for subsets based on the designed comparison in different groups.
+<Descr>
+    Metabolic landscape of single cells in the tumor microenvironment.
+</Descr>
+
+<h2>Workflow of the original analysis</h2>
+<Image src="https://raw.githubusercontent.com/LocasaleLab/Single-Cell-Metabolic-Landscape/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: `subset_by`, usually the clinic groups that bring biological meaning
+(i.e. different timepoints or sample types (tumor/normal)), and `group_by`, usually the cell types.
+</Descr>
+
+<UnorderedList>
+<ListItem>
+    <span class="listitem">MetabolicPathwayActivity (this page)</span>
+    <Tile>
+        <p>Investigating the metabolic pathways of the cells in different subsets and groups.</p>
+        <p>The cells are first subset by subsets and then the metabolic activities are examined for each groups in different subsets.</p>
+        <p> </p>
+        <p>A pathway activity score defined as the relative gene expression value averaged over all genes in the pathway and all cells of the group.</p>
+        <p> </p>
+        <p>For the i-th metabolic gene, we first calculated its mean expression level across cells of the j-th cell group:
+        <Math displayMode>E_{i,j} = \frac{ {\mathop {\sum }\nolimits_{k = 1}^{n_j} g_{i,k}}}{ {n_j}},\,i \in 1 \ldots M,j \in 1 \ldots N</Math>
+        <p>
+            In which n<sub>j</sub> is the number of cells in the j-th cell group, g<sub>i,k</sub> is the expression level of the i-th gene in the k-th cell in this cell group,
+            M is the number of metabolic genes, and N is the number of cell groups. The relative expression level of the i-th gene in the j-th cell group was then
+            defined as the ratio of E<sub>i,j</sub> to its average over all cell groups:
+        </p>
+        <Math displayMode>r_{i,j} = \frac{ {E_{i,j}}}{ {\frac{1}{N}\mathop {\sum }\nolimits_j^N E_{i,j}}}</Math>
+        <p>
+            Here r<sub>i,j</sub> quantifies the relative expression level of gene i in cell group j comparing to the average expression level of this gene in all cell groups.
+            A r<sub>i,j</sub> value &gt;1 means that expression level of gene i is higher in cell group j compared to its average expression level over all cell groups.
+            The pathway activity score for the t-th pathway and the j-th cell group was then defined as the weighted average of r<sub>i,j</sub> over all genes included
+            in this pathway:
+        </p>
+        <Math displayMode>p_{t,j} = \frac{ {\mathop {\sum }\nolimits_{i = 1}^{m_t} w_i \times r_{i,j}}}{ {\mathop {\sum }\nolimits_{i = 1}^{m_t} w_i}}</Math>
+        <p>Where p<sub>t,j</sub> represents the activity of the t-th pathway in the j-th cell group, m<sub>t</sub> is the number of genes in the pathway t, w<sub>i</sub>
+        is the weighting factor equal to the reciprocal of number of pathways that include the i-th gene.
+        To avoid the possibility that pathway activity scores were affected by genes with low expression level or high drop-out rates,
+        we excluded the outliers in each pathway defined by genes with relative expression levels greater than three times 75th percentile or below 1/3 times 25th percentile.
+        Statistical significance of higher or lower pathway activity in a specific cell group was then evaluated by a random permutation test,
+        in which the cell group labels were randomly shuffled for 5000 (for the scRNA datasets) to simulate a null distribution of the pathway activity scores
+        and compare to the pathway activity scores in the original, non-shuffled dataset.
+        For the pathway activity score p<sub>t,j</sub>, we then calculated a p-value defined as the fraction of random pathway activity scores larger than pt,j
+        (if p<sub>t,j</sub> is &gt;1) or smaller than p<sub>t,j</sub> (if p<sub>t,j</sub> is &lt;1) to assess if activity of this pathway is significantly
+        higher or lower in this cell group than average.</p>
+    </Tile>
+</ListItem>
+<ListItem>
+    <a href="?proc=MetabolicPathwayHeterogeneity" class="listitem">MetabolicPathwayHeterogeneity</a>
+    <Tile>
+        <p>Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</p>
+    </Tile>
+</ListItem>
+<ListItem>
+    <a href="?proc=MetabolicFeatures" class="listitem">MetabolicFeatures</a>
+    <Tile>
+        <p>Gene set enrichment analysis against the metabolic pathways for comparisons by different groups in different subsets.</p>
+    </Tile>
+</ListItem>
+</UnorderedList>
 
-</Markdown>
-</div>
-
-{%- 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 {{envs.grouping}}</h{{ h+1 }}>
-  <Image src="{{ssdir | joinpaths: 'KEGGpathway_activity_heatmap.png'}}" />
-
-  <h{{ h+1 }}>Distributions of pathway activities by {{envs.grouping}}</h{{ h+1 }}>
-  <Image src="{{ssdir | joinpaths: 'pathway_activity_violinplot.png'}}" />
-  {%- endfor -%}
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>
 
-  {% 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 -%}
+{%- macro report_job(job, h=1) -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}
-  <h1>{{job.in.sobjfile | stem | escape}}</h1>
+    <h1>{{job.in | attr: "values" | call | first | stem0 | escape}}</h1>
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}
 
-<style>
-
-.markdown-wrap ul {
-    list-style-position: inside;
-    list-style-type: disc;
-    margin-top: 0.2rem;
-}
-
-.markdown-wrap ul li p {
-    padding-left: 1.2rem;
-}
-
-.markdown-wrap ul li > p:first-of-type {
-    padding-left: 0;
-    display: inline;
-}
-</style>

biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte

@@ -1,21 +1,81 @@
-{% from "utils/misc.liq" import report_jobs, table_of_images -%}
-
+{% from "utils/misc.liq" import report_jobs -%}
 <script>
-    import { Image } from "$libs";
+    import { Image, DataTable, Descr } from "$libs";
+    import { Tabs, Tab, TabContent, UnorderedList, ListItem, InlineNotification, Tile } from "$ccs";
 </script>
 
-{%- macro report_job(job, h=2) -%}
-  {%- for ssdir in job.out.outdir | glob: "*" -%}
-  <h{{h}}>{{ ssdir | stem }}</h{{h}}>
+<h1>Introduction</h1>
+
+<Descr>
+    Metabolic landscape of single cells in the tumor microenvironment.
+</Descr>
+
+<h2>Workflow of the original analysis</h2>
+<Image src="https://raw.githubusercontent.com/LocasaleLab/Single-Cell-Metabolic-Landscape/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: `subset_by`, usually the clinic groups that bring biological meaning
+(i.e. different timepoints or sample types (tumor/normal)), and `group_by`, usually the cell types.
+</Descr>
+
+<UnorderedList>
+<ListItem>
+    <a href="?proc=MetabolicPathwayActivity" class="listitem">MetabolicPathwayActivity</a>
+    <Tile>
+    <p>Investigating the metabolic pathways of the cells in different subsets and groups.</p>
+    </Tile>
+</ListItem>
+<ListItem>
+    <span class="listitem">MetabolicPathwayHeterogeneity (this page)</span>
+    <Tile>
+    <p>Showing metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</p>
+    <p>
+        The PCA analysis was applied on normalized expression values.
+        The function prcomp in R was used to perform the PCA analysis.
+        For each metabolic gene, we computed its PCA score defined as the sum of absolute values of the loadings of this gene in the top PCs
+        that in total account for certain variance to measure variability of gene expression across cells.
+        We then sorted the PCA scores of the genes in descending order and applied GSEA analysis to the ranked list of genes to identify metabolic pathways
+        enriched in genes with highest variability.
+    </p>
+    </Tile>
+</ListItem>
+<ListItem>
+    <a href="?proc=MetabolicFeatures" class="listitem">MetabolicFeatures</a>
+    <Tile>
+    <p>Gene set enrichment analysis against the metabolic pathways for comparisons by different groups in different subsets.</p>
+    </Tile>
+</ListItem>
+</UnorderedList>
 
-  <h{{h+1}}>Metabolic pathways enriched in genes with highest contribution to the metabolic heterogeneities</h{{h+1}}>
-  <Image src="{{ssdir | joinpaths: 'pathway_heterogeneity.png'}}" />
+<style>
+.listitem {
+    font-size: large;
+    font-weight: bold;
+    margin: 1rem 0 0.5rem 0;
+    display: inline-block;
+}
+</style>
 
-  {%- endfor -%}
+{%- macro report_job(job, h=1) -%}
+    {{ job | render_job: h=h }}
 {%- endmacro -%}
 
 {%- macro head_job(job) -%}
-  <h1>{{job.in.sobjfile | stem | escape}}</h1>
+    <h1>{{job.in | attr: "values" | call | first | stem0 | escape}}</h1>
 {%- endmacro -%}
 
 {{ report_jobs(jobs, head_job, report_job) }}