make html

unravel/docs/_build/html/_modules/unravel/cluster_stats/mean_IF_summary.html

@@ -366,7 +366,7 @@ <h1>Source code for unravel.cluster_stats.mean_IF_summary</h1><div class="highli
 <span class="sd">    - The first word of the csv inputs is used for the the group names (underscore separated).</span>
 
 <span class="sd">Inputs: </span>
-<span class="sd">    - &lt;asterisk&gt;.csv in the working dir with these columns: &#39;Cluster_ID&#39;, &#39;Mean_IF_Intensity&#39;</span>
+<span class="sd">    - `&lt;asterisk&gt;.csv` in the working dir with these columns: &#39;Cluster_ID&#39;, &#39;Mean_IF_Intensity&#39;</span>
 
 <span class="sd">Prereqs:</span>
 <span class="sd">    - Generate CSV inputs withs ``cluster_IF_mean``</span>

unravel/docs/_build/html/_sources/guide.md.txt

@@ -179,8 +179,8 @@ unravel_commands -m
 - [**cluster_sunburst**](unravel.cluster_stats.sunburst): Create a sunburst plot of regional volumes.
 - [**cluster_find_incongruent_clusters**](unravel.cluster_stats.find_incongruent_clusters): Find clusters where the effect direction does not match the prediction of cluster_fdr (for validation of non-directional p value maps).
 - [**cluster_crop**](unravel.cluster_stats.crop): Crop clusters to a bounding box.
-- [**cluster_mean_IF**](unravel.cluster_stats.cluster_mean_IF): Compute mean immunofluo intensities for each cluster.
-- [**cluster_mean_IF_summary**](unravel.cluster_stats.cluster_mean_IF_summary): Plot mean immunofluo intensities for each cluster.
+- [**cluster_mean_IF**](unravel.cluster_stats.mean_IF): Compute mean immunofluo intensities for each cluster.
+- [**cluster_mean_IF_summary**](unravel.cluster_stats.mean_IF_summary): Plot mean immunofluo intensities for each cluster.
 - [**effect_sizes**](unravel.cluster_stats.effect_sizes.effect_sizes): Calculate effect sizes for clusters.
 - [**effect_sizes_sex_abs**](unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__absolute): Calculate absolute effect sizes by sex.
 - [**effect_sizes_sex_rel**](unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative): Calculate relative effect sizes by sex.

unravel/docs/_build/html/guide.html

@@ -578,8 +578,8 @@ <h2>Common commands<a class="headerlink" href="#common-commands" title="Link to
 <li><p><a class="reference internal" href="unravel/cluster_stats/sunburst.html#unravel-cluster-stats-sunburst"><span class="std std-ref"><strong>cluster_sunburst</strong></span></a>: Create a sunburst plot of regional volumes.</p></li>
 <li><p><a class="reference internal" href="unravel/cluster_stats/find_incongruent_clusters.html#unravel-cluster-stats-find-incongruent-clusters"><span class="std std-ref"><strong>cluster_find_incongruent_clusters</strong></span></a>: Find clusters where the effect direction does not match the prediction of cluster_fdr (for validation of non-directional p value maps).</p></li>
 <li><p><a class="reference internal" href="unravel/cluster_stats/crop.html#unravel-cluster-stats-crop"><span class="std std-ref"><strong>cluster_crop</strong></span></a>: Crop clusters to a bounding box.</p></li>
-<li><p><a class="reference internal" href="#unravel.cluster_stats.cluster_mean_IF"><span class="xref myst"><strong>cluster_mean_IF</strong></span></a>: Compute mean immunofluo intensities for each cluster.</p></li>
-<li><p><a class="reference internal" href="#unravel.cluster_stats.cluster_mean_IF_summary"><span class="xref myst"><strong>cluster_mean_IF_summary</strong></span></a>: Plot mean immunofluo intensities for each cluster.</p></li>
+<li><p><a class="reference internal" href="unravel/cluster_stats/index.html#unravel-cluster-stats-mean-if"><span class="std std-ref"><strong>cluster_mean_IF</strong></span></a>: Compute mean immunofluo intensities for each cluster.</p></li>
+<li><p><a class="reference internal" href="unravel/cluster_stats/mean_IF_summary.html#unravel-cluster-stats-mean-if-summary"><span class="std std-ref"><strong>cluster_mean_IF_summary</strong></span></a>: Plot mean immunofluo intensities for each cluster.</p></li>
 <li><p><a class="reference internal" href="unravel/cluster_stats/effect_sizes/effect_sizes.html#unravel-cluster-stats-effect-sizes-effect-sizes"><span class="std std-ref"><strong>effect_sizes</strong></span></a>: Calculate effect sizes for clusters.</p></li>
 <li><p><a class="reference internal" href="unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__absolute.html#unravel-cluster-stats-effect-sizes-effect-sizes-by-sex-absolute"><span class="std std-ref"><strong>effect_sizes_sex_abs</strong></span></a>: Calculate absolute effect sizes by sex.</p></li>
 <li><p><a class="reference internal" href="unravel/cluster_stats/effect_sizes/effect_sizes_by_sex__relative.html#unravel-cluster-stats-effect-sizes-effect-sizes-by-sex-relative"><span class="std std-ref"><strong>effect_sizes_sex_rel</strong></span></a>: Calculate relative effect sizes by sex.</p></li>

unravel/docs/_build/html/unravel/cluster_stats/mean_IF_summary.html

@@ -512,7 +512,7 @@ <h2>Usage for Tukey’s tests w/ reordering and renaming of conditions:<a class=
 </div>
 <dl class="simple">
 <dt>Inputs:</dt><dd><ul class="simple">
-<li><p>&lt;asterisk&gt;.csv in the working dir with these columns: ‘Cluster_ID’, ‘Mean_IF_Intensity’</p></li>
+<li><p><cite>&lt;asterisk&gt;.csv</cite> in the working dir with these columns: ‘Cluster_ID’, ‘Mean_IF_Intensity’</p></li>
 </ul>
 </dd>
 <dt>Prereqs:</dt><dd><ul class="simple">