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vals committed May 13, 2024
1 parent bd2b56d commit 0ad8493
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46 changes: 23 additions & 23 deletions 201109_Make_records_figure.html
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Expand Up @@ -972,7 +972,7 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
<td>True</td>
</tr>
<tr>
<th>1786</th>
<th>1787</th>
<td>Qiu et al Nature</td>
<td>10.1038/s41586-024-07069-w</td>
<td>Chengxiang Qiu, Beth K. Martin, Ian C. Welsh, ...</td>
Expand All @@ -996,7 +996,7 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
<td>True</td>
</tr>
<tr>
<th>1787</th>
<th>1788</th>
<td>Zhang et al bioRxiv</td>
<td>10.1101/2024.03.01.583001</td>
<td>Zehao Zhang, Chloe Schaefer, Weirong Jiang, Zi...</td>
Expand Down Expand Up @@ -1051,7 +1051,7 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
</div>
</div>
<div class="cell_output docutils container">
<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>(1797, 29)
<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>(1798, 29)
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Expand Down Expand Up @@ -1082,10 +1082,10 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
</div>
</div>
<div class="cell_output docutils container">
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:364: PlotnineWarning: geom_point : Removed 399 rows containing missing values.
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:364: PlotnineWarning: geom_point : Removed 400 rows containing missing values.
</pre></div>
</div>
<a class="reference internal image-reference" href="_images/6090a282b0dc1c21e4d37e69f9464374b0024730f33bc303b725458b102063dd.png"><img alt="_images/6090a282b0dc1c21e4d37e69f9464374b0024730f33bc303b725458b102063dd.png" src="_images/6090a282b0dc1c21e4d37e69f9464374b0024730f33bc303b725458b102063dd.png" style="width: 2000px; height: 700px;" /></a>
<a class="reference internal image-reference" href="_images/c6f41a3b76cfb166665a74aa8c4a99461a058c8b79977c9a4bbfedf54411c9ee.png"><img alt="_images/c6f41a3b76cfb166665a74aa8c4a99461a058c8b79977c9a4bbfedf54411c9ee.png" src="_images/c6f41a3b76cfb166665a74aa8c4a99461a058c8b79977c9a4bbfedf54411c9ee.png" style="width: 2000px; height: 700px;" /></a>
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<div class="cell docutils container">
Expand Down Expand Up @@ -1123,7 +1123,7 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
</div>
</div>
<div class="cell_output docutils container">
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:364: PlotnineWarning: geom_point : Removed 399 rows containing missing values.
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:364: PlotnineWarning: geom_point : Removed 400 rows containing missing values.
</pre></div>
</div>
<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
Expand Down Expand Up @@ -1199,10 +1199,10 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
<span class="g g-Whitespace"> </span><span class="mi">443</span> <span class="c1"># Draw the geoms</span>
<span class="ne">--&gt; </span><span class="mi">444</span> <span class="bp">self</span><span class="o">.</span><span class="n">layers</span><span class="o">.</span><span class="n">draw</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">layout</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:459,</span> in <span class="ni">Layers.draw</span><span class="nt">(self, layout, coord)</span>
<span class="g g-Whitespace"> </span><span class="mi">457</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">start</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="g g-Whitespace"> </span><span class="mi">458</span> <span class="n">l</span><span class="o">.</span><span class="n">zorder</span> <span class="o">=</span> <span class="n">i</span>
<span class="ne">--&gt; </span><span class="mi">459</span> <span class="n">l</span><span class="o">.</span><span class="n">draw</span><span class="p">(</span><span class="n">layout</span><span class="p">,</span> <span class="n">coord</span><span class="p">)</span>
<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:453,</span> in <span class="ni">Layers.draw</span><span class="nt">(self, layout, coord)</span>
<span class="g g-Whitespace"> </span><span class="mi">451</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">start</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="g g-Whitespace"> </span><span class="mi">452</span> <span class="n">l</span><span class="o">.</span><span class="n">zorder</span> <span class="o">=</span> <span class="n">i</span>
<span class="ne">--&gt; </span><span class="mi">453</span> <span class="n">l</span><span class="o">.</span><span class="n">draw</span><span class="p">(</span><span class="n">layout</span><span class="p">,</span> <span class="n">coord</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:367,</span> in <span class="ni">layer.draw</span><span class="nt">(self, layout, coord)</span>
<span class="g g-Whitespace"> </span><span class="mi">364</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">geom</span><span class="o">.</span><span class="n">handle_na</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
Expand All @@ -1229,10 +1229,10 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
<span class="g g-Whitespace"> </span><span class="mi">330</span> <span class="n">gdata</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="ne">--&gt; </span><span class="mi">331</span> <span class="bp">self</span><span class="o">.</span><span class="n">draw_group</span><span class="p">(</span><span class="n">gdata</span><span class="p">,</span> <span class="n">panel_params</span><span class="p">,</span> <span class="n">coord</span><span class="p">,</span> <span class="n">ax</span><span class="p">,</span> <span class="o">**</span><span class="n">params</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/geoms/geom_text.py:280,</span> in <span class="ni">geom_text.draw_group</span><span class="nt">(data, panel_params, coord, ax, **params)</span>
<span class="g g-Whitespace"> </span><span class="mi">277</span> <span class="k">if</span> <span class="s2">&quot;mutation_scale&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">arrowprops</span><span class="p">:</span>
<span class="g g-Whitespace"> </span><span class="mi">278</span> <span class="n">arrowprops</span><span class="p">[</span><span class="s2">&quot;mutation_scale&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s2">&quot;size&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
<span class="ne">--&gt; </span><span class="mi">280</span> <span class="n">adjust_text</span><span class="p">(</span><span class="n">texts</span><span class="p">,</span> <span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">arrowprops</span><span class="o">=</span><span class="n">arrowprops</span><span class="p">,</span> <span class="o">**</span><span class="n">_adjust</span><span class="p">)</span>
<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/geoms/geom_text.py:271,</span> in <span class="ni">geom_text.draw_group</span><span class="nt">(data, panel_params, coord, ax, **params)</span>
<span class="g g-Whitespace"> </span><span class="mi">268</span> <span class="k">if</span> <span class="s2">&quot;mutation_scale&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">arrowprops</span><span class="p">:</span>
<span class="g g-Whitespace"> </span><span class="mi">269</span> <span class="n">arrowprops</span><span class="p">[</span><span class="s2">&quot;mutation_scale&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s2">&quot;size&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
<span class="ne">--&gt; </span><span class="mi">271</span> <span class="n">adjust_text</span><span class="p">(</span><span class="n">texts</span><span class="p">,</span> <span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">arrowprops</span><span class="o">=</span><span class="n">arrowprops</span><span class="p">,</span> <span class="o">**</span><span class="n">_adjust</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/adjustText/__init__.py:635,</span> in <span class="ni">adjust_text</span><span class="nt">(texts, x, y, objects, target_x, target_y, avoid_self, force_text, force_static, force_pull, force_explode, pull_threshold, expand, explode_radius, ensure_inside_axes, expand_axes, only_move, ax, min_arrow_len, time_lim, iter_lim, *args, **kwargs)</span>
<span class="g g-Whitespace"> </span><span class="mi">632</span> <span class="n">text</span><span class="o">.</span><span class="n">set_position</span><span class="p">(</span><span class="n">text_mid</span><span class="p">)</span>
Expand Down Expand Up @@ -1278,7 +1278,7 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
</pre></div>
</div>
<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/IPython/lib/pretty.py:779: FutureWarning: Using repr(plot) to draw and show the plot figure is deprecated and will be removed in a future version. Use plot.show().
/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:364: PlotnineWarning: geom_point : Removed 399 rows containing missing values.
/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:364: PlotnineWarning: geom_point : Removed 400 rows containing missing values.
</pre></div>
</div>
<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
Expand Down Expand Up @@ -1385,10 +1385,10 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
<span class="g g-Whitespace"> </span><span class="mi">443</span> <span class="c1"># Draw the geoms</span>
<span class="ne">--&gt; </span><span class="mi">444</span> <span class="bp">self</span><span class="o">.</span><span class="n">layers</span><span class="o">.</span><span class="n">draw</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">layout</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">coordinates</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:459,</span> in <span class="ni">Layers.draw</span><span class="nt">(self, layout, coord)</span>
<span class="g g-Whitespace"> </span><span class="mi">457</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">start</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="g g-Whitespace"> </span><span class="mi">458</span> <span class="n">l</span><span class="o">.</span><span class="n">zorder</span> <span class="o">=</span> <span class="n">i</span>
<span class="ne">--&gt; </span><span class="mi">459</span> <span class="n">l</span><span class="o">.</span><span class="n">draw</span><span class="p">(</span><span class="n">layout</span><span class="p">,</span> <span class="n">coord</span><span class="p">)</span>
<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:453,</span> in <span class="ni">Layers.draw</span><span class="nt">(self, layout, coord)</span>
<span class="g g-Whitespace"> </span><span class="mi">451</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">start</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
<span class="g g-Whitespace"> </span><span class="mi">452</span> <span class="n">l</span><span class="o">.</span><span class="n">zorder</span> <span class="o">=</span> <span class="n">i</span>
<span class="ne">--&gt; </span><span class="mi">453</span> <span class="n">l</span><span class="o">.</span><span class="n">draw</span><span class="p">(</span><span class="n">layout</span><span class="p">,</span> <span class="n">coord</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/layer.py:367,</span> in <span class="ni">layer.draw</span><span class="nt">(self, layout, coord)</span>
<span class="g g-Whitespace"> </span><span class="mi">364</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">geom</span><span class="o">.</span><span class="n">handle_na</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
Expand All @@ -1415,10 +1415,10 @@ <h1>Make plot highlighting record datasets over time<a class="headerlink" href="
<span class="g g-Whitespace"> </span><span class="mi">330</span> <span class="n">gdata</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="ne">--&gt; </span><span class="mi">331</span> <span class="bp">self</span><span class="o">.</span><span class="n">draw_group</span><span class="p">(</span><span class="n">gdata</span><span class="p">,</span> <span class="n">panel_params</span><span class="p">,</span> <span class="n">coord</span><span class="p">,</span> <span class="n">ax</span><span class="p">,</span> <span class="o">**</span><span class="n">params</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/geoms/geom_text.py:280,</span> in <span class="ni">geom_text.draw_group</span><span class="nt">(data, panel_params, coord, ax, **params)</span>
<span class="g g-Whitespace"> </span><span class="mi">277</span> <span class="k">if</span> <span class="s2">&quot;mutation_scale&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">arrowprops</span><span class="p">:</span>
<span class="g g-Whitespace"> </span><span class="mi">278</span> <span class="n">arrowprops</span><span class="p">[</span><span class="s2">&quot;mutation_scale&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s2">&quot;size&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
<span class="ne">--&gt; </span><span class="mi">280</span> <span class="n">adjust_text</span><span class="p">(</span><span class="n">texts</span><span class="p">,</span> <span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">arrowprops</span><span class="o">=</span><span class="n">arrowprops</span><span class="p">,</span> <span class="o">**</span><span class="n">_adjust</span><span class="p">)</span>
<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/plotnine/geoms/geom_text.py:271,</span> in <span class="ni">geom_text.draw_group</span><span class="nt">(data, panel_params, coord, ax, **params)</span>
<span class="g g-Whitespace"> </span><span class="mi">268</span> <span class="k">if</span> <span class="s2">&quot;mutation_scale&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">arrowprops</span><span class="p">:</span>
<span class="g g-Whitespace"> </span><span class="mi">269</span> <span class="n">arrowprops</span><span class="p">[</span><span class="s2">&quot;mutation_scale&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="s2">&quot;size&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
<span class="ne">--&gt; </span><span class="mi">271</span> <span class="n">adjust_text</span><span class="p">(</span><span class="n">texts</span><span class="p">,</span> <span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">arrowprops</span><span class="o">=</span><span class="n">arrowprops</span><span class="p">,</span> <span class="o">**</span><span class="n">_adjust</span><span class="p">)</span>

<span class="nn">File /opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/adjustText/__init__.py:635,</span> in <span class="ni">adjust_text</span><span class="nt">(texts, x, y, objects, target_x, target_y, avoid_self, force_text, force_static, force_pull, force_explode, pull_threshold, expand, explode_radius, ensure_inside_axes, expand_axes, only_move, ax, min_arrow_len, time_lim, iter_lim, *args, **kwargs)</span>
<span class="g g-Whitespace"> </span><span class="mi">632</span> <span class="n">text</span><span class="o">.</span><span class="n">set_position</span><span class="p">(</span><span class="n">text_mid</span><span class="p">)</span>
Expand Down
Binary file renamed ...64374b0024730f33bc303b725458b102063dd.png → ...a99461a058c8b79977c9a4bbfedf54411c9ee.png
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