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_modules/index.html

@@ -17,7 +17,7 @@
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../_static/documentation_options.js?v=5929fcd5"></script>
-        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />

_modules/starling/starling.html

@@ -17,7 +17,7 @@
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../_static/documentation_options.js?v=5929fcd5"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
@@ -253,8 +253,8 @@ <h1>Source code for starling.starling</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">adata</span><span class="o">.</span><span class="n">uns</span><span class="p">[</span><span class="s2">&quot;init_cell_size_variances&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">init_sv</span><span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="c1"># init_cell_size_centroids = None; init_cell_size_variances = None</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">adata</span><span class="o">.</span><span class="n">varm</span><span class="p">[</span><span class="s2">&quot;init_cell_size_centroids&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">adata</span><span class="o">.</span><span class="n">varm</span><span class="p">[</span><span class="s2">&quot;init_cell_size_variances&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">adata</span><span class="o">.</span><span class="n">uns</span><span class="p">[</span><span class="s2">&quot;init_cell_size_centroids&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">adata</span><span class="o">.</span><span class="n">uns</span><span class="p">[</span><span class="s2">&quot;init_cell_size_variances&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">train_df</span> <span class="o">=</span> <span class="n">utility</span><span class="o">.</span><span class="n">ConcatDataset</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">X</span><span class="p">,</span> <span class="n">tr_fy</span><span class="p">,</span> <span class="n">tr_fl</span><span class="p">])</span>
 
         <span class="c1"># model_params = utility.model_paramters(self.init_e, self.init_v, self.init_s, self.init_sv)</span>

_modules/starling/utility.html

@@ -17,7 +17,7 @@
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
         <script src="../../_static/documentation_options.js?v=5929fcd5"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
@@ -123,7 +123,7 @@ <h1>Source code for starling.utility</h1><div class="highlight"><pre>
 <span class="k">def</span> <span class="nf">init_clustering</span><span class="p">(</span>
     <span class="n">initial_clustering_method</span><span class="p">:</span> <span class="n">Literal</span><span class="p">[</span><span class="s2">&quot;User&quot;</span><span class="p">,</span> <span class="s2">&quot;KM&quot;</span><span class="p">,</span> <span class="s2">&quot;GMM&quot;</span><span class="p">,</span> <span class="s2">&quot;FS&quot;</span><span class="p">,</span> <span class="s2">&quot;PG&quot;</span><span class="p">],</span>
     <span class="n">adata</span><span class="p">:</span> <span class="n">AnnData</span><span class="p">,</span>
-    <span class="n">k</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="kc">None</span><span class="p">],</span>
+    <span class="n">k</span><span class="p">:</span> <span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
     <span class="n">labels</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">AnnData</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Compute initial cluster centroids, variances &amp; labels</span>
@@ -134,7 +134,8 @@ <h1>Source code for starling.utility</h1><div class="highlight"><pre>
 <span class="sd">        ``FS`` (FlowSOM), ``User`` (user-provided), or ``PG`` (PhenoGraph).</span>
 <span class="sd">    :param k: The number of clusters, must be ``n_components`` when ``initial_clustering_method`` is ``GMM`` (required),</span>
 <span class="sd">        ``k`` when ``initial_clustering_method`` is ``KM`` (required), ``k`` when ``initial_clustering_method``</span>
-<span class="sd">        is ``FS`` (required), ``?`` when  ``initial_clustering_method`` is ``PG`` (optional)</span>
+<span class="sd">        is ``FS`` (required), ``?`` when  ``initial_clustering_method`` is ``PG`` (optional), and can be ommited when</span>
+<span class="sd">        ``initial_clustering_method`` is &quot;User&quot;, because user will be passing in their own labels.</span>
 <span class="sd">    :param labels: optional, user-provided labels</span>
 
 <span class="sd">    :raises: ValueError</span>
@@ -152,6 +153,11 @@ <h1>Source code for starling.utility</h1><div class="highlight"><pre>
             <span class="s2">&quot;k cannot be ommitted for KMeans, FlowSOM, or Gaussian Mixture&quot;</span>
         <span class="p">)</span>
 
+    <span class="k">if</span> <span class="n">initial_clustering_method</span> <span class="o">==</span> <span class="s2">&quot;User&quot;</span> <span class="ow">and</span> <span class="n">labels</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+            <span class="s2">&quot;labels must be provided when initial_clustering_method is set to &#39;User&#39;&quot;</span>
+        <span class="p">)</span>
+
     <span class="k">if</span> <span class="n">initial_clustering_method</span> <span class="o">==</span> <span class="s2">&quot;KM&quot;</span><span class="p">:</span>
         <span class="n">kms</span> <span class="o">=</span> <span class="n">KMeans</span><span class="p">(</span><span class="n">k</span><span class="p">)</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">adata</span><span class="o">.</span><span class="n">X</span><span class="p">)</span>
         <span class="n">init_l</span> <span class="o">=</span> <span class="n">kms</span><span class="o">.</span><span class="n">labels_</span>
@@ -175,12 +181,13 @@ <h1>Source code for starling.utility</h1><div class="highlight"><pre>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">init_l</span> <span class="o">=</span> <span class="n">labels</span>
 
-        <span class="n">k</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">init_l</span><span class="p">))</span>
+        <span class="n">classes</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">init_l</span><span class="p">)</span>
+        <span class="n">k</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">classes</span><span class="p">)</span>
         <span class="n">init_e</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">k</span><span class="p">,</span> <span class="n">adata</span><span class="o">.</span><span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
         <span class="n">init_ev</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">k</span><span class="p">,</span> <span class="n">adata</span><span class="o">.</span><span class="n">X</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
-        <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">k</span><span class="p">):</span>
-            <span class="n">init_e</span><span class="p">[</span><span class="n">c</span><span class="p">,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">adata</span><span class="o">.</span><span class="n">X</span><span class="p">[</span><span class="n">init_l</span> <span class="o">==</span> <span class="n">c</span><span class="p">]</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
-            <span class="n">init_ev</span><span class="p">[</span><span class="n">c</span><span class="p">,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">adata</span><span class="o">.</span><span class="n">X</span><span class="p">[</span><span class="n">init_l</span> <span class="o">==</span> <span class="n">c</span><span class="p">]</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">c</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">classes</span><span class="p">):</span>
+            <span class="n">init_e</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">adata</span><span class="o">.</span><span class="n">X</span><span class="p">[</span><span class="n">init_l</span> <span class="o">==</span> <span class="n">c</span><span class="p">]</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+            <span class="n">init_ev</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="p">:]</span> <span class="o">=</span> <span class="n">adata</span><span class="o">.</span><span class="n">X</span><span class="p">[</span><span class="n">init_l</span> <span class="o">==</span> <span class="n">c</span><span class="p">]</span><span class="o">.</span><span class="n">var</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
 
     <span class="k">elif</span> <span class="n">initial_clustering_method</span> <span class="o">==</span> <span class="s2">&quot;FS&quot;</span><span class="p">:</span>
         <span class="c1">## needs to output to csv first</span>

_sources/tutorial/getting-started.ipynb.txt

@@ -19,17 +19,16 @@
    },
    "outputs": [],
    "source": [
-    "%pip install https://github.com/camlab-bioml/starling/archive/main.zip\n",
+    "%pip install biostarling\n",
     "%pip install lightning_lite\n",
     "\n",
     "import anndata as ad\n",
     "import pandas as pd\n",
     "import torch\n",
+    "from starling import starling, utility\n",
     "from lightning_lite import seed_everything\n",
-    "from pytorch_lightning.callbacks import EarlyStopping  # ModelCheckpoint\n",
-    "from pytorch_lightning.loggers import TensorBoardLogger\n",
-    "\n",
-    "from starling import starling, utility"
+    "import pytorch_lightning as pl\n",
+    "\n"
    ]
   },
   {
@@ -169,7 +168,7 @@
    "outputs": [],
    "source": [
     "## log training results via tensorboard\n",
-    "log_tb = TensorBoardLogger(save_dir=\"log\")"
+    "log_tb = pl.logging.TensorBoardLogger(save_dir=\"log\")"
    ]
   },
   {
@@ -196,7 +195,7 @@
    "outputs": [],
    "source": [
     "## set early stopping criterion\n",
-    "cb_early_stopping = EarlyStopping(monitor=\"train_loss\", mode=\"min\", verbose=False)"
+    "cb_early_stopping = pl.callbacks.EarlyStopping(monitor=\"train_loss\", mode=\"min\", verbose=False)"
    ]
   },
   {
@@ -229,7 +228,7 @@
     "## train ST\n",
     "st.train_and_fit(\n",
     "    callbacks=[cb_early_stopping],\n",
-    "    logger=[log_tb],\n",
+    "    #logger=[log_tb],\n",
     ")"
    ]
   },
@@ -448,7 +447,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.9.15"
   }
  },
  "nbformat": 4,

_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/language_data.js

@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer