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docs/Intersection_8hpp_source.html

@@ -140,7 +140,7 @@
 <div class="ttc" id="anamespacesinglepp_html"><div class="ttname"><a href="namespacesinglepp.html">singlepp</a></div><div class="ttdoc">Cell type classification using the SingleR algorithm in C++.</div><div class="ttdef"><b>Definition</b> classify_single.hpp:19</div></div>
 <div class="ttc" id="anamespacesinglepp_html_a22b70c4d5949e28af164723543361214"><div class="ttname"><a href="namespacesinglepp.html#a22b70c4d5949e28af164723543361214">singlepp::intersect_genes</a></div><div class="ttdeci">Intersection&lt; Index_ &gt; intersect_genes(Index_ test_nrow, const Id_ *test_id, Index_ ref_nrow, const Id_ *ref_id)</div><div class="ttdef"><b>Definition</b> Intersection.hpp:50</div></div>
 <div class="ttc" id="anamespacesinglepp_html_a24793af2399b65d4f290e28cc0ef475c"><div class="ttname"><a href="namespacesinglepp.html#a24793af2399b65d4f290e28cc0ef475c">singlepp::Intersection</a></div><div class="ttdeci">std::vector&lt; std::pair&lt; Index_, Index_ &gt; &gt; Intersection</div><div class="ttdef"><b>Definition</b> Intersection.hpp:31</div></div>
-<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:38</div></div>
+<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:40</div></div>
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docs/Markers_8hpp_source.html

@@ -99,14 +99,14 @@
 <div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span> </div>
 <div class="line"><a id="l00014" name="l00014"></a><span class="lineno">   14</span><span class="keyword">namespace </span><a class="code hl_namespace" href="namespacesinglepp.html">singlepp</a> {</div>
 <div class="line"><a id="l00015" name="l00015"></a><span class="lineno">   15</span> </div>
-<div class="line"><a id="l00037" name="l00037"></a><span class="lineno">   37</span><span class="keyword">template</span>&lt;<span class="keyword">typename</span> Index_&gt;</div>
-<div class="line"><a id="l00038" name="l00038"></a><span class="lineno"><a class="line" href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">   38</a></span><span class="keyword">using </span><a class="code hl_typedef" href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">Markers</a> = std::vector&lt;std::vector&lt;std::vector&lt;Index_&gt; &gt; &gt;;</div>
-<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span> </div>
-<div class="line"><a id="l00040" name="l00040"></a><span class="lineno">   40</span>}</div>
+<div class="line"><a id="l00039" name="l00039"></a><span class="lineno">   39</span><span class="keyword">template</span>&lt;<span class="keyword">typename</span> Index_&gt;</div>
+<div class="line"><a id="l00040" name="l00040"></a><span class="lineno"><a class="line" href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">   40</a></span><span class="keyword">using </span><a class="code hl_typedef" href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">Markers</a> = std::vector&lt;std::vector&lt;std::vector&lt;Index_&gt; &gt; &gt;;</div>
 <div class="line"><a id="l00041" name="l00041"></a><span class="lineno">   41</span> </div>
-<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span><span class="preprocessor">#endif</span></div>
+<div class="line"><a id="l00042" name="l00042"></a><span class="lineno">   42</span>}</div>
+<div class="line"><a id="l00043" name="l00043"></a><span class="lineno">   43</span> </div>
+<div class="line"><a id="l00044" name="l00044"></a><span class="lineno">   44</span><span class="preprocessor">#endif</span></div>
 <div class="ttc" id="anamespacesinglepp_html"><div class="ttname"><a href="namespacesinglepp.html">singlepp</a></div><div class="ttdoc">Cell type classification using the SingleR algorithm in C++.</div><div class="ttdef"><b>Definition</b> classify_single.hpp:19</div></div>
-<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:38</div></div>
+<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:40</div></div>
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docs/choose__classic__markers_8hpp_source.html

@@ -324,7 +324,7 @@
 <div class="ttc" id="aMarkers_8hpp_html"><div class="ttname"><a href="Markers_8hpp.html">Markers.hpp</a></div><div class="ttdoc">Define the Markers typedef.</div></div>
 <div class="ttc" id="aclasstatami_1_1Matrix_html"><div class="ttname"><a href="https://tatami-inc.github.io/tatami/classtatami_1_1Matrix.html">tatami::Matrix</a></div></div>
 <div class="ttc" id="anamespacesinglepp_html"><div class="ttname"><a href="namespacesinglepp.html">singlepp</a></div><div class="ttdoc">Cell type classification using the SingleR algorithm in C++.</div><div class="ttdef"><b>Definition</b> classify_single.hpp:19</div></div>
-<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:38</div></div>
+<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:40</div></div>
 <div class="ttc" id="anamespacesinglepp_html_ac26ab7d42558905cab72d85e509cfb0c"><div class="ttname"><a href="namespacesinglepp.html#ac26ab7d42558905cab72d85e509cfb0c">singlepp::number_of_classic_markers</a></div><div class="ttdeci">size_t number_of_classic_markers(size_t num_labels)</div><div class="ttdef"><b>Definition</b> choose_classic_markers.hpp:33</div></div>
 <div class="ttc" id="anamespacesinglepp_html_ae888912441a04acf856e74a9f4a0452b"><div class="ttname"><a href="namespacesinglepp.html#ae888912441a04acf856e74a9f4a0452b">singlepp::choose_classic_markers</a></div><div class="ttdeci">Markers&lt; Index_ &gt; choose_classic_markers(const std::vector&lt; const tatami::Matrix&lt; Value_, Index_ &gt; * &gt; &amp;representatives, const std::vector&lt; const Label_ * &gt; &amp;labels, const ChooseClassicMarkersOptions &amp;options)</div><div class="ttdef"><b>Definition</b> choose_classic_markers.hpp:78</div></div>
 <div class="ttc" id="astructsinglepp_1_1ChooseClassicMarkersOptions_html"><div class="ttname"><a href="structsinglepp_1_1ChooseClassicMarkersOptions.html">singlepp::ChooseClassicMarkersOptions</a></div><div class="ttdoc">Options for choose_classic_markers().</div><div class="ttdef"><b>Definition</b> choose_classic_markers.hpp:40</div></div>

docs/classify__integrated_8hpp_source.html

@@ -198,7 +198,7 @@
 <div class="ttc" id="aclasstatami_1_1Matrix_html"><div class="ttname"><a href="https://tatami-inc.github.io/tatami/classtatami_1_1Matrix.html">tatami::Matrix</a></div></div>
 <div class="ttc" id="anamespacesinglepp_html"><div class="ttname"><a href="namespacesinglepp.html">singlepp</a></div><div class="ttdoc">Cell type classification using the SingleR algorithm in C++.</div><div class="ttdef"><b>Definition</b> classify_single.hpp:19</div></div>
 <div class="ttc" id="anamespacesinglepp_html_a60f705dc3fdc122139e2102713e7ec41"><div class="ttname"><a href="namespacesinglepp.html#a60f705dc3fdc122139e2102713e7ec41">singlepp::classify_integrated</a></div><div class="ttdeci">void classify_integrated(const tatami::Matrix&lt; Value_, Index_ &gt; &amp;test, const std::vector&lt; const Label_ * &gt; &amp;assigned, const TrainedIntegrated&lt; Index_ &gt; &amp;trained, ClassifyIntegratedBuffers&lt; RefLabel_, Float_ &gt; &amp;buffers, const ClassifyIntegratedOptions&lt; Float_ &gt; &amp;options)</div><div class="ttdoc">Integrate classifications from multiple references.</div><div class="ttdef"><b>Definition</b> classify_integrated.hpp:125</div></div>
-<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:38</div></div>
+<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:40</div></div>
 <div class="ttc" id="astructsinglepp_1_1ClassifyIntegratedBuffers_html"><div class="ttname"><a href="structsinglepp_1_1ClassifyIntegratedBuffers.html">singlepp::ClassifyIntegratedBuffers</a></div><div class="ttdoc">Output buffers for classify_single().</div><div class="ttdef"><b>Definition</b> classify_integrated.hpp:58</div></div>
 <div class="ttc" id="astructsinglepp_1_1ClassifyIntegratedBuffers_html_a51dd05dee04d9d73f1ad6d62655ca1e1"><div class="ttname"><a href="structsinglepp_1_1ClassifyIntegratedBuffers.html#a51dd05dee04d9d73f1ad6d62655ca1e1">singlepp::ClassifyIntegratedBuffers::best</a></div><div class="ttdeci">RefLabel_ * best</div><div class="ttdef"><b>Definition</b> classify_integrated.hpp:63</div></div>
 <div class="ttc" id="astructsinglepp_1_1ClassifyIntegratedBuffers_html_a7307840e67b7743f985ad4c780090168"><div class="ttname"><a href="structsinglepp_1_1ClassifyIntegratedBuffers.html#a7307840e67b7743f985ad4c780090168">singlepp::ClassifyIntegratedBuffers::delta</a></div><div class="ttdeci">Float_ * delta</div><div class="ttdef"><b>Definition</b> classify_integrated.hpp:78</div></div>

docs/classify__single_8hpp_source.html

@@ -246,7 +246,7 @@
 <div class="line"><a id="l00309" name="l00309"></a><span class="lineno">  309</span><span class="preprocessor">#endif</span></div>
 <div class="ttc" id="aclasstatami_1_1Matrix_html"><div class="ttname"><a href="https://tatami-inc.github.io/tatami/classtatami_1_1Matrix.html">tatami::Matrix</a></div></div>
 <div class="ttc" id="anamespacesinglepp_html"><div class="ttname"><a href="namespacesinglepp.html">singlepp</a></div><div class="ttdoc">Cell type classification using the SingleR algorithm in C++.</div><div class="ttdef"><b>Definition</b> classify_single.hpp:19</div></div>
-<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:38</div></div>
+<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:40</div></div>
 <div class="ttc" id="anamespacesinglepp_html_ad7d214a5da53597d24dec5cec59e3beb"><div class="ttname"><a href="namespacesinglepp.html#ad7d214a5da53597d24dec5cec59e3beb">singlepp::classify_single_intersect</a></div><div class="ttdeci">void classify_single_intersect(const tatami::Matrix&lt; Value_, Index_ &gt; &amp;test, const TrainedSingleIntersect&lt; Index_, Float_ &gt; &amp;trained, const ClassifySingleBuffers&lt; Label_, Float_ &gt; &amp;buffers, const ClassifySingleOptions&lt; Float_ &gt; &amp;options)</div><div class="ttdef"><b>Definition</b> classify_single.hpp:169</div></div>
 <div class="ttc" id="anamespacesinglepp_html_ae8772734badf4a09d6c285b9b98295ec"><div class="ttname"><a href="namespacesinglepp.html#ae8772734badf4a09d6c285b9b98295ec">singlepp::classify_single</a></div><div class="ttdeci">void classify_single(const tatami::Matrix&lt; Value_, Index_ &gt; &amp;test, const TrainedSingle&lt; Index_, Float_ &gt; &amp;trained, const ClassifySingleBuffers&lt; Label_, Float_ &gt; &amp;buffers, const ClassifySingleOptions&lt; Float_ &gt; &amp;options)</div><div class="ttdoc">Implements the SingleR algorithm for automated annotation of single-cell RNA-seq data.</div><div class="ttdef"><b>Definition</b> classify_single.hpp:130</div></div>
 <div class="ttc" id="astructsinglepp_1_1ClassifySingleBuffers_html"><div class="ttname"><a href="structsinglepp_1_1ClassifySingleBuffers.html">singlepp::ClassifySingleBuffers</a></div><div class="ttdoc">Output buffers for classify_single().</div><div class="ttdef"><b>Definition</b> classify_single.hpp:63</div></div>

docs/index.html

@@ -104,7 +104,7 @@ <h1>Quick start</h1>
 <div class="line"><span class="comment">// Running the classification on the test matrix.</span></div>
 <div class="line"><a class="code hl_typedef" href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::ClassifySingleOptions&lt;double&gt;</a> class_opt;</div>
 <div class="line"><span class="keyword">auto</span> res = <a class="code hl_typedef" href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::classify_single&lt;int&gt;</a>(test_mat, trained, class_opt);</div>
-<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:38</div></div>
+<div class="ttc" id="anamespacesinglepp_html_a87e4be0939142d883ad98944e6336a5c"><div class="ttname"><a href="namespacesinglepp.html#a87e4be0939142d883ad98944e6336a5c">singlepp::Markers</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; std::vector&lt; Index_ &gt; &gt; &gt; Markers</div><div class="ttdef"><b>Definition</b> Markers.hpp:40</div></div>
 <div class="ttc" id="anamespacesinglepp_html_abcea821671f9339e4e933be2ed123c6e"><div class="ttname"><a href="namespacesinglepp.html#abcea821671f9339e4e933be2ed123c6e">singlepp::train_single</a></div><div class="ttdeci">TrainedSingle&lt; Index_, Float_ &gt; train_single(const tatami::Matrix&lt; Value_, Index_ &gt; &amp;ref, const Label_ *labels, Markers&lt; Index_ &gt; markers, const TrainSingleOptions&lt; Index_, Float_ &gt; &amp;options)</div><div class="ttdef"><b>Definition</b> train_single.hpp:180</div></div>
 <div class="ttc" id="asinglepp_8hpp_html"><div class="ttname"><a href="singlepp_8hpp.html">singlepp.hpp</a></div><div class="ttdoc">Umbrella header for the singlepp library.</div></div>
 </div><!-- fragment --><p>See the <a href="https://singler-inc.github.io/singlepp">reference documentation</a> for more details.</p>