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Merge pull request #328 from monarch-initiative/add_mf_stats_to_cohor…
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Counting male and female individuals for CohortViewer
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@pnrobinson
pnrobinson authored Oct 28, 2024
2 parents 7110b09 + 0c109b6 commit e1f7ab3
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84 changes: 52 additions & 32 deletions docs/report/tbx5_cohort_info.html
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<body>
<h1>GPSEA cohort analysis</h1>
<p>Successfully loaded 156 individuals.</p>
<p>Successfully loaded 156 individuals. 46 were recorded as male, 56 as female,
and 54 as unknown sex. 156 were reported to be alive at the time of last
encounter, and 0 were deceased. 1 had disease onset information
and 51 had information about the age at last encounter. In the cohort,
there were a total of 117 HPO terms used for annotation.

</p>

<p>No errors encountered.</p>


<table>
<caption style="color: black;">
<h3>Top 10 HPO Terms</h3>
A total of 116 HPO terms were used to annotated the cohort.
A total of 117 HPO terms were used to annotated the cohort.
</caption>
<tbody>
<tr class="strng">
Expand Down Expand Up @@ -106,14 +112,14 @@ <h3>Top 10 HPO Terms</h3>
</tr>

<tr>
<td class="lft">Absent thumb</td>
<td>HP:0009777</td>
<td class="lft">Short thumb</td>
<td>HP:0009778</td>
<td>32</td>
</tr>

<tr>
<td class="lft">Short thumb</td>
<td>HP:0009778</td>
<td class="lft">Absent thumb</td>
<td>HP:0009777</td>
<td>32</td>
</tr>

Expand Down Expand Up @@ -144,14 +150,16 @@ <h3>Top 10 HPO Terms</h3>
</tbody>
</table>



<table>
<caption style="color: black;">
<h3>Top 10 Variants</h3>
Variants are shown according to NM_181486.4. A total of 156 unique variants were identified in the cohort.
Variants are shown according to NM_181486.4. A total of 53 unique variants were identified in the cohort.
</caption>
<tbody>
<tr class="strng">
<th>Count</th>
<th>Seen in <em>n</em> individuals</th>
<th class="lft">Variant key</th>
<th>Variant Name</th>
<th>Protein Variant</th>
Expand Down Expand Up @@ -190,6 +198,14 @@ <h3>Top 10 Variants</h3>
<td>STOP_GAINED</td>
</tr>

<tr>
<td>5</td>
<td class="lft">12_114399514_114399514_A_C</td>
<td>c.361T>G</td>
<td>p.Trp121Gly</td>
<td>MISSENSE_VARIANT, SPLICE_REGION_VARIANT</td>
</tr>

<tr>
<td>5</td>
<td class="lft">12_114398682_114398682_C_CG</td>
Expand All @@ -206,14 +222,6 @@ <h3>Top 10 Variants</h3>
<td>FRAMESHIFT_VARIANT</td>
</tr>

<tr>
<td>5</td>
<td class="lft">12_114399514_114399514_A_C</td>
<td>c.361T>G</td>
<td>p.Trp121Gly</td>
<td>MISSENSE_VARIANT, SPLICE_REGION_VARIANT</td>
</tr>

<tr>
<td>4</td>
<td class="lft">12_114385474_114385474_A_G</td>
Expand All @@ -232,10 +240,10 @@ <h3>Top 10 Variants</h3>

<tr>
<td>4</td>
<td class="lft">12_114366360_114366360_C_T</td>
<td>c.787G>A</td>
<td>p.Val263Met</td>
<td>MISSENSE_VARIANT</td>
<td class="lft">12_114403798_114403798_G_GC</td>
<td>c.100dup</td>
<td>p.Ala34GlyfsTer27</td>
<td>FRAMESHIFT_VARIANT</td>
</tr>

</tbody>
Expand Down Expand Up @@ -268,61 +276,73 @@ <h3>Variant categories for NM_181486.4</h3>
<tr class="strng">
<th class="lft">Variant effect</th>
<th>Annotation Count</th>
<th>Percent</th>
</tr>

<tr>
<td class="lft">FRAMESHIFT_VARIANT</td>
<td>38</td>
<td class="lft">MISSENSE_VARIANT</td>
<td>85</td>
<td>50%</td>
</tr>

<tr>
<td class="lft">MISSENSE_VARIANT</td>
<td>85</td>
<td class="lft">FRAMESHIFT_VARIANT</td>
<td>38</td>
<td>22%</td>
</tr>

<tr>
<td class="lft">STOP_GAINED</td>
<td>19</td>
<td>11%</td>
</tr>

<tr>
<td class="lft">SPLICE_REGION_VARIANT</td>
<td>10</td>
<td>6%</td>
</tr>

<tr>
<td class="lft">SPLICE_ACCEPTOR_VARIANT</td>
<td>2</td>
<td class="lft">SPLICE_DONOR_VARIANT</td>
<td>7</td>
<td>4%</td>
</tr>

<tr>
<td class="lft">SPLICE_DONOR_VARIANT</td>
<td>7</td>
<td class="lft">INFRAME_INSERTION</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">SPLICE_DONOR_5TH_BASE_VARIANT</td>
<td class="lft">STOP_RETAINED_VARIANT</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">INTRON_VARIANT</td>
<td class="lft">SPLICE_ACCEPTOR_VARIANT</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">INFRAME_INSERTION</td>
<td class="lft">SPLICE_DONOR_5TH_BASE_VARIANT</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">STOP_RETAINED_VARIANT</td>
<td class="lft">INTRON_VARIANT</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">INFRAME_DELETION</td>
<td>1</td>
<td>1%</td>
</tr>

</tbody>
Expand Down
2 changes: 1 addition & 1 deletion docs/user-guide/exploratory.rst
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Expand Up @@ -111,7 +111,7 @@ with an overview about the HPO terms, variants, diseases, and variant effects th
.. doctest:: exploratory
:hide:

>>> report.write('docs/user-guide/reports/tbx5_cohort_INFO.html') # doctest: +SKIP
>>> report.write('docs/user-guide/reports/tbx5_cohort_info.html') # doctest: +SKIP


Distribution of variants across protein domains
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90 changes: 55 additions & 35 deletions docs/user-guide/reports/tbx5_cohort_info.html
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Original file line number Diff line number Diff line change
Expand Up @@ -64,15 +64,21 @@

<body>
<h1>GPSEA cohort analysis</h1>
<p>Successfully loaded 156 individuals.</p>
<p>Successfully loaded 156 individuals. 46 were recorded as male, 56 as female,
and 54 as unknown sex. 156 were reported to be alive at the time of last
encounter, and 0 were deceased. 1 had disease onset information
and 51 had information about the age at last encounter. In the cohort,
there were a total of 117 HPO terms used for annotation.

</p>

<p>No errors encountered.</p>


<table>
<caption style="color: black;">
<h3>Top 10 HPO Terms</h3>
A total of 116 HPO terms were used to annotated the cohort.
A total of 117 HPO terms were used to annotated the cohort.
</caption>
<tbody>
<tr class="strng">
Expand Down Expand Up @@ -106,14 +112,14 @@ <h3>Top 10 HPO Terms</h3>
</tr>

<tr>
<td class="lft">Short thumb</td>
<td>HP:0009778</td>
<td class="lft">Absent thumb</td>
<td>HP:0009777</td>
<td>32</td>
</tr>

<tr>
<td class="lft">Absent thumb</td>
<td>HP:0009777</td>
<td class="lft">Short thumb</td>
<td>HP:0009778</td>
<td>32</td>
</tr>

Expand Down Expand Up @@ -144,14 +150,16 @@ <h3>Top 10 HPO Terms</h3>
</tbody>
</table>



<table>
<caption style="color: black;">
<h3>Top 10 Variants</h3>
Variants are shown according to NM_181486.4. A total of 156 unique variants were identified in the cohort.
Variants are shown according to NM_181486.4. A total of 53 unique variants were identified in the cohort.
</caption>
<tbody>
<tr class="strng">
<th>Count</th>
<th>Seen in <em>n</em> individuals</th>
<th class="lft">Variant key</th>
<th>Variant Name</th>
<th>Protein Variant</th>
Expand Down Expand Up @@ -190,14 +198,6 @@ <h3>Top 10 Variants</h3>
<td>STOP_GAINED</td>
</tr>

<tr>
<td>5</td>
<td class="lft">12_114399514_114399514_A_C</td>
<td>c.361T>G</td>
<td>p.Trp121Gly</td>
<td>MISSENSE_VARIANT, SPLICE_REGION_VARIANT</td>
</tr>

<tr>
<td>5</td>
<td class="lft">12_114398682_114398682_C_CG</td>
Expand All @@ -206,6 +206,14 @@ <h3>Top 10 Variants</h3>
<td>FRAMESHIFT_VARIANT</td>
</tr>

<tr>
<td>5</td>
<td class="lft">12_114399514_114399514_A_C</td>
<td>c.361T>G</td>
<td>p.Trp121Gly</td>
<td>MISSENSE_VARIANT, SPLICE_REGION_VARIANT</td>
</tr>

<tr>
<td>5</td>
<td class="lft">12_114403792_114403792_C_CG</td>
Expand All @@ -216,10 +224,10 @@ <h3>Top 10 Variants</h3>

<tr>
<td>4</td>
<td class="lft">12_114385474_114385474_A_G</td>
<td>c.755+2T>C</td>
<td>None</td>
<td>SPLICE_DONOR_VARIANT</td>
<td class="lft">12_114385522_114385522_G_A</td>
<td>c.709C>T</td>
<td>p.Arg237Trp</td>
<td>MISSENSE_VARIANT</td>
</tr>

<tr>
Expand Down Expand Up @@ -268,61 +276,73 @@ <h3>Variant categories for NM_181486.4</h3>
<tr class="strng">
<th class="lft">Variant effect</th>
<th>Annotation Count</th>
<th>Percent</th>
</tr>

<tr>
<td class="lft">MISSENSE_VARIANT</td>
<td>85</td>
<td>50%</td>
</tr>

<tr>
<td class="lft">FRAMESHIFT_VARIANT</td>
<td>38</td>
<td>22%</td>
</tr>

<tr>
<td class="lft">SPLICE_REGION_VARIANT</td>
<td>10</td>
<td class="lft">STOP_GAINED</td>
<td>19</td>
<td>11%</td>
</tr>

<tr>
<td class="lft">INFRAME_DELETION</td>
<td>1</td>
<td class="lft">SPLICE_REGION_VARIANT</td>
<td>10</td>
<td>6%</td>
</tr>

<tr>
<td class="lft">INFRAME_INSERTION</td>
<td>2</td>
<td class="lft">SPLICE_DONOR_VARIANT</td>
<td>7</td>
<td>4%</td>
</tr>

<tr>
<td class="lft">STOP_RETAINED_VARIANT</td>
<td class="lft">SPLICE_ACCEPTOR_VARIANT</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">STOP_GAINED</td>
<td>19</td>
<td class="lft">SPLICE_DONOR_5TH_BASE_VARIANT</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">SPLICE_DONOR_VARIANT</td>
<td>7</td>
<td class="lft">INTRON_VARIANT</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">SPLICE_ACCEPTOR_VARIANT</td>
<td class="lft">INFRAME_INSERTION</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">SPLICE_DONOR_5TH_BASE_VARIANT</td>
<td class="lft">STOP_RETAINED_VARIANT</td>
<td>2</td>
<td>1%</td>
</tr>

<tr>
<td class="lft">INTRON_VARIANT</td>
<td>2</td>
<td class="lft">INFRAME_DELETION</td>
<td>1</td>
<td>1%</td>
</tr>

</tbody>
Expand Down
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