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rerun pipeline and refresh results
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@gwaybio
gwaybio committed Oct 10, 2018
1 parent 7f0ec87 commit aba8144
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Binary file modified figures/NF1_confidence_scores.pdf
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171 changes: 157 additions & 14 deletions html/2.evaluate-classifier-pdx.html
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Expand Up @@ -12061,12 +12061,12 @@ <h2 id="Load-Status-Matrix">Load Status Matrix<a class="anchor-link" href="#Load
ALK 18
KRAS 16
NF1 12
DMD 10
NRAS 10
DMD 10
CIC 8
SOS1 7
PTPN11 4
HRAS 4
PTPN11 4
BRAF 3
Name: Hugo_Symbol, dtype: int64</pre>
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Expand Down Expand Up @@ -12103,13 +12103,13 @@ <h2 id="Load-Status-Matrix">Load Status Matrix<a class="anchor-link" href="#Load
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<pre>Missense_Mutation 112
Shallow_Del 17
Nonsense_Mutation 13
Fusion 13
Nonsense_Mutation 13
Frame_Shift_Del 5
Splice_Site 3
Frame_Shift_Ins 3
In_Frame_Del 1
Deep_Del 1
In_Frame_Del 1
Name: Variant_Classification, dtype: int64</pre>
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Expand Down Expand Up @@ -12150,18 +12150,18 @@ <h2 id="Load-Status-Matrix">Load Status Matrix<a class="anchor-link" href="#Load
Ewing Sarcoma 12
Ph-likeALL 7
Embryonal Rhabdomyosarcoma 6
MLL-ALL 4
Medulloblastoma 4
Alveolar Rhabdomyosarcoma 4
MLL-ALL 4
Wilms 4
T-ALL 4
Wilms 4
Astrocytoma 3
ATRT 3
ETP-ALL 2
Other Sarcoma 2
Colon Carcinoma 1
Small Cell Carcinoma 1
Rhabdoid 1
Colon Carcinoma 1
Name: Histology.Detailed, dtype: int64</pre>
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Expand Down Expand Up @@ -12712,12 +12712,155 @@ <h2 id="Extract-Gene-Status">Extract Gene Status<a class="anchor-link" href="#Ex
<span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">ras_status</span> <span class="o">=</span> <span class="n">full_status_df</span><span class="o">.</span><span class="n">loc</span><span class="p">[:,</span> <span class="n">ras_genes</span><span class="p">]</span>
<span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="s1">&#39;columns&#39;</span><span class="p">))</span>
<span class="p">)</span>

<span class="n">full_status_df</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
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<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}

.dataframe tbody tr th {
vertical-align: top;
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.dataframe thead th {
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<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>Model</th>
<th>ALK</th>
<th>BRAF</th>
<th>CIC</th>
<th>DMD</th>
<th>HRAS</th>
<th>KRAS</th>
<th>NF1</th>
<th>NRAS</th>
<th>PTPN11</th>
<th>SOS1</th>
<th>TP53</th>
<th>Histology_Full</th>
<th>ras_status</th>
</tr>
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<th>0</th>
<td>ALL-03</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>MLL-ALL</td>
<td>1</td>
</tr>
<tr>
<th>1</th>
<td>ALL-07</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>BCP-ALL</td>
<td>1</td>
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<th>2</th>
<td>ALL-08</td>
<td>0</td>
<td>0</td>
<td>0</td>
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<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>T-ALL</td>
<td>1</td>
</tr>
<tr>
<th>3</th>
<td>ALL-108</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>Ph-likeALL</td>
<td>1</td>
</tr>
<tr>
<th>4</th>
<td>ALL-115</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>0</td>
<td>1</td>
<td>BCP-ALL</td>
<td>0</td>
</tr>
</tbody>
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Expand Down Expand Up @@ -12917,21 +13060,21 @@ <h2 id="Load-Clinical-Data-Information">Load Clinical Data Information<a class="
Ewing Sarcoma 10
MLL-ALL 10
ATRT 8
Alveolar Rhabdomyosarcoma 7
PNET 7
Alveolar Rhabdomyosarcoma 7
Embryonal Rhabdomyosarcoma 7
ETP-ALL 6
Ependymoma 6
Glioblastoma 6
Ependymoma 6
Rhabdoid 5
Ph+-ALL 3
Other Sarcoma 3
Ph+-ALL 3
Astrocytoma 2
Small Cell Carcinoma 2
Other Renal 2
DIPG 2
Small Cell Carcinoma 2
Astrocytoma 2
CNS germinoma 1
Colon Carcinoma 1
CNS germinoma 1
Name: Histology-Detailed, dtype: int64</pre>
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Expand Down Expand Up @@ -13967,7 +14110,7 @@ <h2 id="Write-output-files-for-downstream-analysis">Write output files for downs
<span class="n">scores_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s2">&quot;results&quot;</span><span class="p">,</span> <span class="s2">&quot;classifier_scores_with_clinical_and_alterations.tsv&quot;</span><span class="p">)</span>
<span class="n">genes</span> <span class="o">=</span> <span class="n">ras_genes</span> <span class="o">+</span> <span class="p">[</span><span class="s1">&#39;TP53&#39;</span><span class="p">]</span>

<span class="n">scores_df</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s1">&#39;Model_x&#39;</span><span class="p">,</span> <span class="s1">&#39;Model_y&#39;</span><span class="p">,</span> <span class="s1">&#39;Histology_Full&#39;</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="s1">&#39;columns&#39;</span><span class="p">)</span>
<span class="n">scores_df</span> <span class="o">=</span> <span class="n">scores_df</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s1">&#39;Model_x&#39;</span><span class="p">,</span> <span class="s1">&#39;Model_y&#39;</span><span class="p">,</span> <span class="s1">&#39;Histology_Full&#39;</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="s1">&#39;columns&#39;</span><span class="p">)</span>
<span class="n">scores_df</span><span class="p">[</span><span class="n">genes</span><span class="p">]</span> <span class="o">=</span> <span class="n">scores_df</span><span class="p">[</span><span class="n">genes</span><span class="p">]</span><span class="o">.</span><span class="n">fillna</span><span class="p">(</span><span class="n">value</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>

<span class="n">scores_df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="s1">&#39;sample_id&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">scores_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s1">&#39;</span><span class="se">\t</span><span class="s1">&#39;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
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8 changes: 4 additions & 4 deletions html/3.explore-variants.html
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Expand Up @@ -12007,13 +12007,13 @@ <h2 id="Output">Output<a class="anchor-link" href="#Output">&#182;</a></h2><p>Th
<th>RNA Part of PPTC</th>
<th>Model Part of PPTC</th>
<th>...</th>
<th>HRAS</th>
<th>KRAS</th>
<th>NF1</th>
<th>NRAS</th>
<th>PTPN11</th>
<th>SOS1</th>
<th>TP53</th>
<th>Histology_Full</th>
<th>ras_status</th>
<th>tp53_status</th>
<th>nf1_status</th>
Expand All @@ -12039,7 +12039,7 @@ <h2 id="Output">Output<a class="anchor-link" href="#Output">&#182;</a></h2><p>Th
<td>0.0</td>
<td>0.0</td>
<td>0.0</td>
<td>NaN</td>
<td>0.0</td>
<td>0</td>
<td>0</td>
<td>0</td>
Expand All @@ -12063,14 +12063,14 @@ <h2 id="Output">Output<a class="anchor-link" href="#Output">&#182;</a></h2><p>Th
<td>0.0</td>
<td>0.0</td>
<td>0.0</td>
<td>MLL-ALL</td>
<td>0.0</td>
<td>1</td>
<td>0</td>
<td>0</td>
</tr>
</tbody>
</table>
<p>2 rows × 42 columns</p>
<p>2 rows × 39 columns</p>
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