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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../tutorial5/">Tutorial 5: Creating a mosaic map</a></li>
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  <section id="slideflow-slidemap">
<h1>slideflow.SlideMap<a class="headerlink" href="#slideflow-slidemap" title="Permalink to this heading">¶</a></h1>
<p><a class="reference internal" href="#slideflow.SlideMap" title="slideflow.SlideMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.SlideMap</span></code></a> assists with visualizing tiles and slides in two-dimensional space.</p>
<p>Once a model has been trained, tile-level predictions and intermediate layer activations can be calculated
across an entire dataset with <a class="reference internal" href="../dataset_features/#slideflow.DatasetFeatures" title="slideflow.DatasetFeatures"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.DatasetFeatures</span></code></a>.
The <a class="reference internal" href="#slideflow.SlideMap" title="slideflow.SlideMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.SlideMap</span></code></a> class can then perform dimensionality reduction on these dataset-wide
activations, plotting tiles and slides in two-dimensional space. Visualizing the distribution and clustering
of tile-level and slide-level layer activations can help reveal underlying structures in the dataset and shared
visual features among classes.</p>
<p>The primary method of use is first generating an <a class="reference internal" href="../dataset_features/#slideflow.DatasetFeatures" title="slideflow.DatasetFeatures"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.DatasetFeatures</span></code></a> from a trained
model, then using <a class="reference internal" href="../dataset_features/#slideflow.DatasetFeatures.map_activations" title="slideflow.DatasetFeatures.map_activations"><code class="xref py py-meth docutils literal notranslate"><span class="pre">slideflow.DatasetFeatures.map_activations()</span></code></a>, which returns an instance of
<a class="reference internal" href="#slideflow.SlideMap" title="slideflow.SlideMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.SlideMap</span></code></a>.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ftrs</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">DatasetFeatures</span><span class="p">(</span><span class="n">model</span><span class="o">=</span><span class="s1">&#39;/path/&#39;</span><span class="p">,</span> <span class="o">...</span><span class="p">)</span>
<span class="n">slide_map</span> <span class="o">=</span> <span class="n">ftrs</span><span class="o">.</span><span class="n">map_activations</span><span class="p">()</span>
</pre></div>
</div>
<p>Alternatively, if you would like to map slides from a dataset in two-dimensional space using pre-calculated <em>x</em> and <em>y</em>
coordinates, you can use the <code class="xref py py-meth docutils literal notranslate"><span class="pre">sldieflow.SlideMap.from_xy()</span></code> class method. In addition to X and Y, this method
requires supplying tile-level metadata in the form of a list of dicts. Each dict must contain the name of the origin
slide and the tile index in the slide TFRecord.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">x</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="o">...</span><span class="p">)</span>
<span class="n">y</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="o">...</span><span class="p">)</span>
<span class="n">slides</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;slide1&#39;</span><span class="p">,</span> <span class="s1">&#39;slide1&#39;</span><span class="p">,</span> <span class="s1">&#39;slide5&#39;</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span>
<span class="n">slide_map</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">SlideMap</span><span class="o">.</span><span class="n">from_xy</span><span class="p">(</span><span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">y</span><span class="p">,</span> <span class="n">slides</span><span class="o">=</span><span class="n">slides</span><span class="p">)</span>
</pre></div>
</div>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.SlideMap">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SlideMap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parametric_umap</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/stats/slidemap/#SlideMap"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.SlideMap" title="Permalink to this definition">¶</a></dt>
<dd><p>Two-dimensional slide map for visualization &amp; backend for mosaic maps.</p>
<p>Slides are mapped in 2D either explicitly with pre-specified coordinates,
or with dimensionality reduction from post-convolutional layer weights,
provided from <a class="reference internal" href="../dataset_features/#slideflow.DatasetFeatures" title="slideflow.DatasetFeatures"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.DatasetFeatures</span></code></a>.</p>
<p>Backend for mapping slides into two dimensional space. Can use a
DatasetFeatures object to map slides according to UMAP of features, or
map according to pre-specified coordinates.</p>
<p>Can be initialized with three methods: from precalculated X/Y
coordinates, from a DatasetFeatures object, or from a saved map.</p>
<dl>
<dt>Examples</dt><dd><p>Build a SlideMap from a DatasetFeatures object</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">dts_ftrs</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">DatasetFeatures</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">dataset</span><span class="p">)</span>
<span class="n">slidemap</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">SlideMap</span><span class="o">.</span><span class="n">from_features</span><span class="p">(</span><span class="n">dts_ftrs</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Build a SlideMap from prespecified coordinates</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">x</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="o">...</span><span class="p">)</span>
<span class="n">y</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="o">...</span><span class="p">)</span>
<span class="n">slides</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;slide1&#39;</span><span class="p">,</span> <span class="s1">&#39;slide1&#39;</span><span class="p">,</span> <span class="s1">&#39;slide5&#39;</span><span class="p">,</span> <span class="o">...</span><span class="p">]</span>
<span class="n">slidemap</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">SlideMap</span><span class="o">.</span><span class="n">from_xy</span><span class="p">(</span>
    <span class="n">x</span><span class="o">=</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">y</span><span class="p">,</span> <span class="n">slides</span><span class="o">=</span><span class="n">slides</span>
<span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
<p>Load a saved SlideMap</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">slidemap</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">SlideMap</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s1">&#39;map.parquet&#39;</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>slides</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – List of slide names</p>
</dd>
</dl>
</dd></dl>

<section id="methods">
<h2>Methods<a class="headerlink" href="#methods" title="Permalink to this heading">¶</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.activations">
<span class="sig-name descname"><span class="pre">activations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="headerlink" href="#slideflow.SlideMap.activations" title="Permalink to this definition">¶</a></dt>
<dd><p>Return associated DatasetFeatures activations as a numpy array
corresponding to the points on this SlideMap.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.build_mosaic">
<span class="sig-name descname"><span class="pre">build_mosaic</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tfrecords</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="../mosaic/#slideflow.Mosaic" title="slideflow.mosaic.Mosaic"><span class="pre">Mosaic</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.build_mosaic" title="Permalink to this definition">¶</a></dt>
<dd><p>Build a mosaic map.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>tfrecords</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em><em>, </em><em>optional</em>) – List of tfrecord paths. If SlideMap
was created using DatasetFeatures, this argument is not required.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>num_tiles_x</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Mosaic map grid size. Defaults to 50.</p></li>
<li><p><strong>tile_select</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – ‘first’, ‘nearest’, or ‘centroid’.
Determines how to choose a tile for display on each grid space.
If ‘first’, will display the first valid tile in a grid space
(fastest; recommended). If ‘nearest’, will display tile nearest
to center of grid space. If ‘centroid’, for each grid, will
calculate which tile is nearest to centroid tile_meta.
Defaults to ‘nearest’.</p></li>
<li><p><strong>tile_meta</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Tile metadata, used for tile_select.
Dictionary should have slide names as keys, mapped to list of
metadata (length of list = number of tiles in slide).
Defaults to None.</p></li>
<li><p><strong>normalizer</strong> ((str or <a class="reference internal" href="../norm/#slideflow.norm.StainNormalizer" title="slideflow.norm.StainNormalizer"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.norm.StainNormalizer</span></code></a>), optional) – Normalization strategy to use on image tiles. Defaults to None.</p></li>
<li><p><strong>normalizer_source</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Stain normalization preset or
path to a source image. Valid presets include ‘v1’, ‘v2’, and
‘v3’. If None, will use the default present (‘v3’).
Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.cluster">
<span class="sig-name descname"><span class="pre">cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_clusters</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.cluster" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs K-means clustering on data and adds to metadata labels.</p>
<p>Clusters are saved to self.data[‘cluster’]. Requires that SlideMap
was generated via DatasetFeatures.</p>
<dl>
<dt>Examples</dt><dd><p>Perform K-means clustering and apply cluster labels.</p>
<blockquote>
<div><p>slidemap.cluster(n_clusters=5)
slidemap.plot()</p>
</div></blockquote>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>n_clusters</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of clusters for K means clustering.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.neighbors">
<span class="sig-name descname"><span class="pre">neighbors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide_categories</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">algorithm</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'kd_tree'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'map'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pca_dim</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.neighbors" title="Permalink to this definition">¶</a></dt>
<dd><dl class="simple">
<dt>Calculates neighbors among tiles in this map, assigning neighboring</dt><dd><p>statistics to tile metadata ‘num_unique_neighbors’ and
‘percent_matching_categories’.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slide_categories</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Maps slides to categories.
Defaults to None. If provided, will be used to calculate
‘percent_matching_categories’ statistic.</p></li>
<li><p><strong>algorithm</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – NearestNeighbor algorithm, either
‘kd_tree’, ‘ball_tree’, or ‘brute’. Defaults to ‘kd_tree’.</p></li>
<li><p><strong>method</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Either ‘map’, ‘pca’, or ‘features’. How
neighbors are determined. If ‘map’, calculates neighbors based
on UMAP coordinates. If ‘features’, calculates neighbors on the
full feature space. If ‘pca’, reduces features into <cite>pca_dim</cite>
space. Defaults to ‘map’.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.filter">
<span class="sig-name descname"><span class="pre">filter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slides</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.filter" title="Permalink to this definition">¶</a></dt>
<dd><p>Filters map to only show tiles from the given slides.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>slides</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – List of slide names.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.umap_transform">
<span class="sig-name descname"><span class="pre">umap_transform</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">array</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dim</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_neighbors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_dist</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metric</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'cosine'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="headerlink" href="#slideflow.SlideMap.umap_transform" title="Permalink to this definition">¶</a></dt>
<dd><p>Transforms a given array using UMAP projection. If a UMAP has not
yet been fit, this will fit a new UMAP on the given data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>array</strong> (<em>np.ndarray</em>) – Array to transform with UMAP dimensionality
reduction.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>dim</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Number of dimensions for UMAP. Defaults to 2.</p></li>
<li><p><strong>n_neighbors</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Number of neighbors for UMAP
algorithm. Defaults to 50.</p></li>
<li><p><strong>min_dist</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Minimum distance argument for UMAP
algorithm. Defaults to 0.1.</p></li>
<li><p><strong>metric</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Metric for UMAP algorithm. Defaults to
‘cosine’.</p></li>
<li><p><strong>**kwargs</strong> (<em>optional</em>) – Additional keyword arguments for the
UMAP function.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.label">
<span class="sig-name descname"><span class="pre">label</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">meta</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">translate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.label" title="Permalink to this definition">¶</a></dt>
<dd><p>Displays each point labeled by tile metadata (e.g. ‘predicted_class’)</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>meta</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Data column from which to assign labels.</p></li>
<li><p><strong>translate</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – If provided, will translate the
read metadata through this dictionary.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.label_by_preds">
<span class="sig-name descname"><span class="pre">label_by_preds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.label_by_preds" title="Permalink to this definition">¶</a></dt>
<dd><p>Displays each point with label equal to the prediction value (from 0-1)</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Logit index.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.label_by_slide">
<span class="sig-name descname"><span class="pre">label_by_slide</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide_labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.label_by_slide" title="Permalink to this definition">¶</a></dt>
<dd><dl class="simple">
<dt>Displays each point as the name of the corresponding slide.</dt><dd><p>If slide_labels is provided, will use this dict to label slides.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>slide_labels</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Dict mapping slide names to labels.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.label_by_uncertainty">
<span class="sig-name descname"><span class="pre">label_by_uncertainty</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.label_by_uncertainty" title="Permalink to this definition">¶</a></dt>
<dd><p>Labels each point with the tile-level uncertainty, if available.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Uncertainty index. Defaults to 0.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.load">
<span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.SlideMap.load" title="Permalink to this definition">¶</a></dt>
<dd><p>Load a previously saved SlideMap (UMAP and coordinates).</p>
<p>Loads a <code class="docutils literal notranslate"><span class="pre">SlideMap</span></code> previously saved with <code class="docutils literal notranslate"><span class="pre">SlideMap.save()</span></code>.</p>
<p>Expects a directory with <code class="docutils literal notranslate"><span class="pre">slidemap.parquet</span></code>, <code class="docutils literal notranslate"><span class="pre">range_clip.npz</span></code>,
and either <code class="docutils literal notranslate"><span class="pre">umap.pkl</span></code> (non-parametric models) or a folder named
<code class="docutils literal notranslate"><span class="pre">parametric_model</span></code>.</p>
<dl>
<dt>Examples</dt><dd><p>Save a SlideMap, then load it.</p>
<blockquote>
<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">slidemap</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s1">&#39;/directory/&#39;</span><span class="p">)</span>
<span class="n">new_slidemap</span> <span class="o">=</span> <span class="n">sf</span><span class="o">.</span><span class="n">SlideMap</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s1">&#39;/directory/&#39;</span><span class="p">)</span>
</pre></div>
</div>
</div></blockquote>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory from which to load a previously saved UMAP.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.load_coordinates">
<span class="sig-name descname"><span class="pre">load_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.load_coordinates" title="Permalink to this definition">¶</a></dt>
<dd><p>Load coordinates from parquet file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Path to parquet file (.parquet) with SlideMap
coordinates.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.load_umap">
<span class="sig-name descname"><span class="pre">load_umap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">umap.UMAP</span></span></span><a class="headerlink" href="#slideflow.SlideMap.load_umap" title="Permalink to this definition">¶</a></dt>
<dd><p>Load only a UMAP model and not slide coordinates or range_clip.npz.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to either umap.pkl or directory with saved
parametric UMAP.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.plot">
<span class="sig-name descname"><span class="pre">plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subsample</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmap</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xlim</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(-0.05,</span> <span class="pre">1.05)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylim</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(-0.05,</span> <span class="pre">1.05)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xlabel</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylabel</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">legend</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Axes</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">loc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'center</span> <span class="pre">right'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">categorical</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'auto'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">legend_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Dict" title="(in Python v3.12)"><span class="pre">Dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">scatter_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Plots calculated map.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>subsample</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Subsample to only include this many
tiles on plot. Defaults to None.</p></li>
<li><p><strong>title</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Title for plot.</p></li>
<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Dict mapping labels to colors.</p></li>
<li><p><strong>xlim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – List of float indicating limit for x-axis.
Defaults to (-0.05, 1.05).</p></li>
<li><p><strong>ylim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – List of float indicating limit for y-axis.
Defaults to (-0.05, 1.05).</p></li>
<li><p><strong>xlabel</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Label for x axis. Defaults to None.</p></li>
<li><p><strong>ylabel</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Label for y axis. Defaults to None.</p></li>
<li><p><strong>legend</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Title for legend. Defaults to None.</p></li>
<li><p><strong>ax</strong> (<em>matplotlib.axes.Axes</em><em>, </em><em>optional</em>) – Figure axis. If not supplied,
will prepare a new figure axis.</p></li>
<li><p><strong>loc</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Location for legend, as defined by
matplotlib.axes.Axes.legend(). Defaults to ‘center right’.</p></li>
<li><p><strong>ncol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Number of columns in legend, as defined
by matplotlib.axes.Axes.legend(). Defaults to 1.</p></li>
<li><p><strong>categorical</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Specify whether labels are categorical.
Determines the colormap.  Defaults to ‘auto’ (will attempt to
automatically determine from the labels).</p></li>
<li><p><strong>legend_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Dictionary of additional keyword
arguments to the matplotlib.axes.Axes.legend() function.</p></li>
<li><p><strong>**scatter_kwargs</strong> (<em>optional</em>) – Additional keyword arguments to the
seaborn scatterplot function.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.plot_3d">
<span class="sig-name descname"><span class="pre">plot_3d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">z</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">feature</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subsample</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fig</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Figure</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.plot_3d" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a plot of a 3D umap, with the 3rd dimension representing
values provided by argument “z”.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>z</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – Values for z axis. Must supply z or feature.
Defaults to None.</p></li>
<li><p><strong>feature</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Int, feature to plot on 3rd axis.
Must supply z or feature. Defaults to None.</p></li>
<li><p><strong>subsample</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Subsample to only include this many
tiles on plot. Defaults to None.</p></li>
<li><p><strong>fig</strong> (<em>matplotlib.figure.Figure</em><em>, </em><em>optional</em>) – Figure. If not supplied,
will prepare a new figure.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.save">
<span class="sig-name descname"><span class="pre">save</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dpi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.SlideMap.save" title="Permalink to this definition">¶</a></dt>
<dd><p>Save UMAP, plot, coordinates, and normalization values to a directory.</p>
<p>The UMAP, plot, coordinates, and normalization values can all be
loaded from this directory after saving with <code class="docutils literal notranslate"><span class="pre">sf.SlideMap.load(path)</span></code>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory in which to save the plot and UMAP.
The UMAP image will be saved with the filename “slidemap.png”.</p></li>
<li><p><strong>dpi</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – DPI for final image. Defaults to 300.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>subsample</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Subsample to only include this many
tiles on plot. Defaults to None.</p></li>
<li><p><strong>title</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Title for plot.</p></li>
<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Dict mapping labels to colors.</p></li>
<li><p><strong>xlim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – List of float indicating limit for x-axis.
Defaults to (-0.05, 1.05).</p></li>
<li><p><strong>ylim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – List of float indicating limit for y-axis.
Defaults to (-0.05, 1.05).</p></li>
<li><p><strong>xlabel</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Label for x axis. Defaults to None.</p></li>
<li><p><strong>ylabel</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Label for y axis. Defaults to None.</p></li>
<li><p><strong>legend</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Title for legend. Defaults to None.</p></li>
<li><p><strong>**scatter_kwargs</strong> (<em>optional</em>) – Additional keyword arguments to the
seaborn scatterplot function.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.save_3d">
<span class="sig-name descname"><span class="pre">save_3d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dpi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.SlideMap.save_3d" title="Permalink to this definition">¶</a></dt>
<dd><p>Save 3D plot of slide map.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – _description_</p></li>
<li><p><strong>dpi</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – _description_. Defaults to 300.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>z</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – Values for z axis. Must supply z or feature.
Defaults to None.</p></li>
<li><p><strong>feature</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Int, feature to plot on 3rd axis.
Must supply z or feature. Defaults to None.</p></li>
<li><p><strong>subsample</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Subsample to only include this many
tiles on plot. Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.save_plot">
<span class="sig-name descname"><span class="pre">save_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dpi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">300</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.SlideMap.save_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Save plot of slide map.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – File path to save the image.</p></li>
<li><p><strong>dpi</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – DPI for final image. Defaults to 300.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>subsample</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Subsample to only include this many
tiles on plot. Defaults to None.</p></li>
<li><p><strong>title</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Title for plot.</p></li>
<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Dict mapping labels to colors.</p></li>
<li><p><strong>xlim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – List of float indicating limit for x-axis.
Defaults to (-0.05, 1.05).</p></li>
<li><p><strong>ylim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>, </em><em>optional</em>) – List of float indicating limit for y-axis.
Defaults to (-0.05, 1.05).</p></li>
<li><p><strong>xlabel</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Label for x axis. Defaults to None.</p></li>
<li><p><strong>ylabel</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Label for y axis. Defaults to None.</p></li>
<li><p><strong>legend</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Title for legend. Defaults to None.</p></li>
<li><p><strong>**scatter_kwargs</strong> (<em>optional</em>) – Additional keyword arguments to the
seaborn scatterplot function.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.save_coordinates">
<span class="sig-name descname"><span class="pre">save_coordinates</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.save_coordinates" title="Permalink to this definition">¶</a></dt>
<dd><p>Save coordinates only to parquet file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Save coordinates to this location.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.save_umap">
<span class="sig-name descname"><span class="pre">save_umap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.save_umap" title="Permalink to this definition">¶</a></dt>
<dd><p>Save UMAP, coordinates, and normalization information to a directory.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Save UMAP and coordinates to this directory.
Coordinates will be saved in this directory with the filename
<code class="docutils literal notranslate"><span class="pre">slidemap.parquet</span></code> Model will be saved as umap.pkl (parametric)
or model.pkl (parametric).</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.SlideMap.save_encoder">
<span class="sig-name descname"><span class="pre">save_encoder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.SlideMap.save_encoder" title="Permalink to this definition">¶</a></dt>
<dd><p>Save Parametric UMAP encoder only.</p>
</dd></dl>

</section>
</section>


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              <ul>
<li><a class="reference internal" href="#">slideflow.SlideMap</a><ul>
<li><a class="reference internal" href="#slideflow.SlideMap"><code class="docutils literal notranslate"><span class="pre">SlideMap</span></code></a></li>
<li><a class="reference internal" href="#methods">Methods</a><ul>
<li><a class="reference internal" href="#slideflow.SlideMap.activations"><code class="docutils literal notranslate"><span class="pre">activations()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.build_mosaic"><code class="docutils literal notranslate"><span class="pre">build_mosaic()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.cluster"><code class="docutils literal notranslate"><span class="pre">cluster()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.neighbors"><code class="docutils literal notranslate"><span class="pre">neighbors()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.filter"><code class="docutils literal notranslate"><span class="pre">filter()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.umap_transform"><code class="docutils literal notranslate"><span class="pre">umap_transform()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.label"><code class="docutils literal notranslate"><span class="pre">label()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.label_by_preds"><code class="docutils literal notranslate"><span class="pre">label_by_preds()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.label_by_slide"><code class="docutils literal notranslate"><span class="pre">label_by_slide()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.label_by_uncertainty"><code class="docutils literal notranslate"><span class="pre">label_by_uncertainty()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.load"><code class="docutils literal notranslate"><span class="pre">load()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.load_coordinates"><code class="docutils literal notranslate"><span class="pre">load_coordinates()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.load_umap"><code class="docutils literal notranslate"><span class="pre">load_umap()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.plot"><code class="docutils literal notranslate"><span class="pre">plot()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.plot_3d"><code class="docutils literal notranslate"><span class="pre">plot_3d()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.save"><code class="docutils literal notranslate"><span class="pre">save()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.save_3d"><code class="docutils literal notranslate"><span class="pre">save_3d()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.save_plot"><code class="docutils literal notranslate"><span class="pre">save_plot()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.save_coordinates"><code class="docutils literal notranslate"><span class="pre">save_coordinates()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.save_umap"><code class="docutils literal notranslate"><span class="pre">save_umap()</span></code></a></li>
<li><a class="reference internal" href="#slideflow.SlideMap.save_encoder"><code class="docutils literal notranslate"><span class="pre">save_encoder()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>

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