Deployed 7c15716 with MkDocs version: 1.6.0

api/lineagetree/index.html

@@ -1827,8 +1827,8 @@ <h1 id="b-cell-lineage-tree">B cell Lineage Tree<a class="headerlink" href="#b-c
 <span class="sd">        ----------</span>
 <span class="sd">        outpath : str</span>
 <span class="sd">            the path to file the files should be written.  </span>
-<span class="sd">        clonotype : Clonotype, optional</span>
-<span class="sd">            the corresponding clonotype object for the lineage tree.  </span>
+<span class="sd">        isotype_encoding : list, optional</span>
+<span class="sd">            the ordered isotype labels  </span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">tree_label</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="n">tree_label</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
@@ -3693,17 +3693,17 @@ <h2 id="tribal.LineageTree.write" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>clonotype</code></td>
+            <td><code>isotype_encoding</code></td>
             <td>
-                  <code><a class="autorefs autorefs-internal" title="tribal.clonotype.Clonotype" href="../clonotype/#tribal.Clonotype">Clonotype</a></code>
+                  <code>list</code>
             </td>
             <td>
               <div class="doc-md-description">
-                <p>the corresponding clonotype object for the lineage tree.</p>
+                <p>the ordered isotype labels</p>
               </div>
             </td>
             <td>
-                <em>required</em>
+                  <code>None</code>
             </td>
           </tr>
       </tbody>
@@ -3756,8 +3756,8 @@ <h2 id="tribal.LineageTree.write" class="doc doc-heading">
 <span class="sd">    ----------</span>
 <span class="sd">    outpath : str</span>
 <span class="sd">        the path to file the files should be written.  </span>
-<span class="sd">    clonotype : Clonotype, optional</span>
-<span class="sd">        the corresponding clonotype object for the lineage tree.  </span>
+<span class="sd">    isotype_encoding : list, optional</span>
+<span class="sd">        the ordered isotype labels  </span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">if</span> <span class="n">tree_label</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
         <span class="n">tree_label</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>

api/lineagetreelist/index.html

@@ -1027,8 +1027,8 @@ <h1 id="b-cell-lineage-tree">B cell Lineage Tree<a class="headerlink" href="#b-c
 <span class="sd">        ----------</span>
 <span class="sd">        outpath : str</span>
 <span class="sd">            the path to where the files should be written.</span>
-<span class="sd">        clonotypes : dict</span>
-<span class="sd">            the corresponding Clonotype object for the LineageTreeList</span>
+<span class="sd">        isotype_encoding : list</span>
+<span class="sd">            the ordered isotype labeles</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">lt</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">lt</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">outpath</span><span class="p">,</span><span class="n">isotype_encoding</span><span class="o">=</span><span class="n">isotype_encoding</span><span class="p">,</span> <span class="n">tree_label</span><span class="o">=</span><span class="n">i</span><span class="p">)</span>
@@ -1623,17 +1623,17 @@ <h2 id="tribal.LineageTreeList.write_all" class="doc doc-heading">
             </td>
           </tr>
           <tr class="doc-section-item">
-            <td><code>clonotypes</code></td>
+            <td><code>isotype_encoding</code></td>
             <td>
-                  <code>dict</code>
+                  <code>list</code>
             </td>
             <td>
               <div class="doc-md-description">
-                <p>the corresponding Clonotype object for the LineageTreeList</p>
+                <p>the ordered isotype labeles</p>
               </div>
             </td>
             <td>
-                <em>required</em>
+                  <code>None</code>
             </td>
           </tr>
       </tbody>
@@ -1659,8 +1659,8 @@ <h2 id="tribal.LineageTreeList.write_all" class="doc doc-heading">
 <span class="sd">    ----------</span>
 <span class="sd">    outpath : str</span>
 <span class="sd">        the path to where the files should be written.</span>
-<span class="sd">    clonotypes : dict</span>
-<span class="sd">        the corresponding Clonotype object for the LineageTreeList</span>
+<span class="sd">    isotype_encoding : list</span>
+<span class="sd">        the ordered isotype labeles</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">lt</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">lt</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">outpath</span><span class="p">,</span><span class="n">isotype_encoding</span><span class="o">=</span><span class="n">isotype_encoding</span><span class="p">,</span> <span class="n">tree_label</span><span class="o">=</span><span class="n">i</span><span class="p">)</span>

setup/cli/index.html

@@ -838,9 +838,9 @@ <h4 id="input">Input<a class="headerlink" href="#input" title="Permanent link">&
 <p class="admonition-title">isotype labeling</p>
 <p>Be sure that the labels used in the encoding file exactly match the labeling syntax in the input data. There is no standard convention for isotype labels,  e.g., IgM, M, IghM and IGHM, and therefore the convention must be provided by the user. </p>
 </div>
-<p>### Output</p>
+<p>#### Output</p>
 <p>The main output from the <code>preprocess</code> sub-command is the a pickled dictionary storing <code>Clonotype</code> objects for each retained clonotype in the data. This output file will be used as the input to the <code>fit</code> sub-command. </p>
-<p>### Example</p>
+<p>#### Example</p>
 <p>Here is an example of how to run the preprocess sub-command.</p>
 <div class="highlight"><pre><span></span><code><span class="w"> </span>$<span class="w"> </span>tribal<span class="w"> </span>preprocess<span class="w"> </span>-d<span class="w"> </span>data.csv<span class="w"> </span>-r<span class="w"> </span>roots.csv<span class="w"> </span>-e<span class="w"> </span>isotypes.txt<span class="w"> </span>-j<span class="w"> </span><span class="m">4</span><span class="w"> </span>--min-size<span class="w"> </span><span class="m">4</span><span class="w"> </span>--dataframe<span class="w"> </span>filtered.csv<span class="w"> </span>-o<span class="w"> </span>clonotypes.pkl<span class="w"> </span>-v
 </code></pre></div>

setup/package/index.html

@@ -904,7 +904,7 @@ <h3 id="exploring-and-visualizing-the-inferred-b-cell-lineage-trees">Exploring a
 <p><code>tribal fit</code> returns a list of all optimal B cell lineage trees for each clonotype. 
 Specifically, in the above examples <code>best_trees</code> is a dictionary, with clonotype as key, of <a href="../../api/lineagetreelist/">LineageTreeLists</a>. </p>
 <p>A B cell lineage tree for tribal is a rooted tree with nodes labeled by BCR sequences (concentated heavy and optional light chains) and by isotypes. The <a href="../../api/lineagetree/">LineageTree</a> class also holds the current  SHM parsimony score (<code>shm_obj</code>) and CSR likelihood (<code>csr_obj</code>). </p>
-<p>A <code>LineageTree</code> can be visualized as a <code>png</code> or <code>pdf</code> via the <a href="../api/lineage_tree.md">draw</a> function.  Nodes are colored by the isotype via the default <code>color_encoding</code>. </p>
+<p>A <code>LineageTree</code> can be visualized as a <code>png</code> or <code>pdf</code> via the <a href="../../api/lineagetree/">draw</a> function.  Nodes are colored by the isotype via the default <code>color_encoding</code>. </p>
 <div class="highlight"><pre><span></span><code> <span class="n">color_encoding</span> <span class="o">=</span>  <span class="p">{</span>
                 <span class="o">-</span><span class="mi">1</span><span class="p">:</span> <span class="s2">&quot;#FFFFFF&quot;</span><span class="p">,</span>
                 <span class="mi">0</span> <span class="p">:</span> <span class="s2">&quot;#808080&quot;</span><span class="p">,</span>
@@ -1052,7 +1052,8 @@ <h3 id="functionality-of-a-lineagetreelist">Functionality of a LineageTreeList<a
 </code></pre></div>
 <p>Lastly, a CSV file with the objective values of each <a href="../../api/lineagetree/">LineageTree</a> in the list can be written.</p>
 <div class="highlight"><pre><span></span><code><span class="kn">from</span> <span class="nn">tribal</span> <span class="kn">import</span> <span class="n">lineage_tree_list</span>
-<span class="n">lineage_tree_list</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;objectives.csv&quot;</span><span class="p">)</span>
+<span class="n">isotypes</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;IGHM&#39;</span><span class="p">,</span> <span class="s1">&#39;IGHG3&#39;</span><span class="p">,</span> <span class="s1">&#39;IGHG1&#39;</span><span class="p">,</span> <span class="s1">&#39;IGHA1&#39;</span><span class="p">,</span><span class="s1">&#39;IGHG2&#39;</span><span class="p">,</span><span class="s1">&#39;IGHG4&#39;</span><span class="p">,</span><span class="s1">&#39;IGHE&#39;</span><span class="p">,</span><span class="s1">&#39;IGHA2&#39;</span><span class="p">]</span>
+<span class="n">lineage_tree_list</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;objectives.csv&quot;</span><span class="p">,</span> <span class="n">isotype_encoding</span><span class="o">=</span><span class="n">isotypes</span><span class="p">)</span>
 </code></pre></div>