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17 changes: 7 additions & 10 deletions docs/aggregate__across__cells_8hpp.html
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<div class="textblock"><code>#include &lt;algorithm&gt;</code><br />
<code>#include &lt;vector&gt;</code><br />
<code>#include &quot;<a class="elRef" href="https://tatami-inc.github.io/tatami/tatami_8hpp.html">tatami/tatami.hpp</a>&quot;</code><br />
<code>#include &quot;tatami_stats/tatami_stats.hpp&quot;</code><br />
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16 changes: 7 additions & 9 deletions docs/aggregate__across__cells_8hpp__incl.map
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2 changes: 1 addition & 1 deletion docs/aggregate__across__cells_8hpp__incl.md5
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533 changes: 275 additions & 258 deletions docs/aggregate__across__cells_8hpp_source.html
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247 changes: 131 additions & 116 deletions docs/aggregate__across__genes_8hpp_source.html
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2 changes: 1 addition & 1 deletion docs/clean__factor_8hpp_source.html
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<div class="line"><a id="l00068" name="l00068"></a><span class="lineno"> 68</span>}</div>
<div class="line"><a id="l00069" name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a id="l00070" name="l00070"></a><span class="lineno"> 70</span><span class="preprocessor">#endif</span></div>
<div class="ttc" id="anamespacescran__aggregate_html"><div class="ttname"><a href="namespacescran__aggregate.html">scran_aggregate</a></div><div class="ttdoc">Aggregate single-cell expression values.</div><div class="ttdef"><b>Definition</b> aggregate_across_cells.hpp:15</div></div>
<div class="ttc" id="anamespacescran__aggregate_html"><div class="ttname"><a href="namespacescran__aggregate.html">scran_aggregate</a></div><div class="ttdoc">Aggregate single-cell expression values.</div><div class="ttdef"><b>Definition</b> aggregate_across_cells.hpp:14</div></div>
<div class="ttc" id="anamespacescran__aggregate_html_a2324eaab6a361f7f767204b62a79764b"><div class="ttname"><a href="namespacescran__aggregate.html#a2324eaab6a361f7f767204b62a79764b">scran_aggregate::clean_factor</a></div><div class="ttdeci">std::vector&lt; Factor_ &gt; clean_factor(size_t n, const Factor_ *factor, Output_ *cleaned)</div><div class="ttdef"><b>Definition</b> clean_factor.hpp:33</div></div>
</div><!-- fragment --></div><!-- contents -->
<!-- start footer part -->
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2 changes: 1 addition & 1 deletion docs/combine__factors_8hpp_source.html
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<div class="line"><a id="l00206" name="l00206"></a><span class="lineno"> 206</span> </div>
<div class="line"><a id="l00207" name="l00207"></a><span class="lineno"> 207</span><span class="preprocessor">#endif</span></div>
<div class="ttc" id="aclean__factor_8hpp_html"><div class="ttname"><a href="clean__factor_8hpp.html">clean_factor.hpp</a></div><div class="ttdoc">Clean up a categorical factor.</div></div>
<div class="ttc" id="anamespacescran__aggregate_html"><div class="ttname"><a href="namespacescran__aggregate.html">scran_aggregate</a></div><div class="ttdoc">Aggregate single-cell expression values.</div><div class="ttdef"><b>Definition</b> aggregate_across_cells.hpp:15</div></div>
<div class="ttc" id="anamespacescran__aggregate_html"><div class="ttname"><a href="namespacescran__aggregate.html">scran_aggregate</a></div><div class="ttdoc">Aggregate single-cell expression values.</div><div class="ttdef"><b>Definition</b> aggregate_across_cells.hpp:14</div></div>
<div class="ttc" id="anamespacescran__aggregate_html_a0712c37387535ba42349ae78cd6fd8ff"><div class="ttname"><a href="namespacescran__aggregate.html#a0712c37387535ba42349ae78cd6fd8ff">scran_aggregate::combine_factors_unused</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; Factor_ &gt; &gt; combine_factors_unused(size_t n, const std::vector&lt; std::pair&lt; const Factor_ *, Number_ &gt; &gt; &amp;factors, Combined_ *combined)</div><div class="ttdef"><b>Definition</b> combine_factors.hpp:146</div></div>
<div class="ttc" id="anamespacescran__aggregate_html_a2324eaab6a361f7f767204b62a79764b"><div class="ttname"><a href="namespacescran__aggregate.html#a2324eaab6a361f7f767204b62a79764b">scran_aggregate::clean_factor</a></div><div class="ttdeci">std::vector&lt; Factor_ &gt; clean_factor(size_t n, const Factor_ *factor, Output_ *cleaned)</div><div class="ttdef"><b>Definition</b> clean_factor.hpp:33</div></div>
<div class="ttc" id="anamespacescran__aggregate_html_ac709e5530c7cb6b488e6b727fe91b890"><div class="ttname"><a href="namespacescran__aggregate.html#ac709e5530c7cb6b488e6b727fe91b890">scran_aggregate::combine_factors</a></div><div class="ttdeci">std::vector&lt; std::vector&lt; Factor_ &gt; &gt; combine_factors(size_t n, const std::vector&lt; const Factor_ * &gt; &amp;factors, Combined_ *combined)</div><div class="ttdef"><b>Definition</b> combine_factors.hpp:40</div></div>
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6 changes: 3 additions & 3 deletions docs/index.html
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Expand Up @@ -98,9 +98,9 @@ <h1>Quick start</h1>
<div class="line">res.sums[0]; <span class="comment">// vector of sums for the first group across genes.</span></div>
<div class="line">res.detected; <span class="comment">// vector of vectors of the number of detected cells per gene.</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="anamespacescran__aggregate_html_a76e8390729e70654df46d322d2e119ff"><div class="ttname"><a href="namespacescran__aggregate.html#a76e8390729e70654df46d322d2e119ff">scran_aggregate::aggregate_across_cells</a></div><div class="ttdeci">void aggregate_across_cells(const tatami::Matrix&lt; Data_, Index_ &gt; &amp;input, const Factor_ *factor, const AggregateAcrossCellsBuffers&lt; Sum_, Detected_ &gt; &amp;buffers, const AggregateAcrossCellsOptions &amp;options)</div><div class="ttdef"><b>Definition</b> aggregate_across_cells.hpp:268</div></div>
<div class="ttc" id="anamespacescran__aggregate_html_a76e8390729e70654df46d322d2e119ff"><div class="ttname"><a href="namespacescran__aggregate.html#a76e8390729e70654df46d322d2e119ff">scran_aggregate::aggregate_across_cells</a></div><div class="ttdeci">void aggregate_across_cells(const tatami::Matrix&lt; Data_, Index_ &gt; &amp;input, const Factor_ *factor, const AggregateAcrossCellsBuffers&lt; Sum_, Detected_ &gt; &amp;buffers, const AggregateAcrossCellsOptions &amp;options)</div><div class="ttdef"><b>Definition</b> aggregate_across_cells.hpp:285</div></div>
<div class="ttc" id="ascran__aggregate_8hpp_html"><div class="ttname"><a href="scran__aggregate_8hpp.html">scran_aggregate.hpp</a></div><div class="ttdoc">Aggregate single-cell expression values.</div></div>
<div class="ttc" id="astructscran__aggregate_1_1AggregateAcrossCellsOptions_html"><div class="ttname"><a href="structscran__aggregate_1_1AggregateAcrossCellsOptions.html">scran_aggregate::AggregateAcrossCellsOptions</a></div><div class="ttdoc">Options for aggregate_across_cells().</div><div class="ttdef"><b>Definition</b> aggregate_across_cells.hpp:20</div></div>
<div class="ttc" id="astructscran__aggregate_1_1AggregateAcrossCellsOptions_html"><div class="ttname"><a href="structscran__aggregate_1_1AggregateAcrossCellsOptions.html">scran_aggregate::AggregateAcrossCellsOptions</a></div><div class="ttdoc">Options for aggregate_across_cells().</div><div class="ttdef"><b>Definition</b> aggregate_across_cells.hpp:19</div></div>
</div><!-- fragment --><p>The array of groupings should contain integer assignments to groups 0, 1, 2, etc. For more complex groupings defined from combinations of multiple factors, the <code>combine_factors()</code> utility will create group assignments from unique combinations of those factors:</p>
<div class="fragment"><div class="line">std::vector&lt;int&gt; grouping1 { 0, 0, 1, 1, 2, 2 };</div>
<div class="line">std::vector&lt;int&gt; grouping2 { 0, 1, 0, 1, 0, 1 };</div>
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<div class="line"> g_opt</div>
<div class="line">);</div>
<div class="line">g_res.sum[0]; <span class="comment">// vector of sums for set 1 in each cell.</span></div>
<div class="ttc" id="anamespacescran__aggregate_html_a8c5e32aa2efd50f80d02fcfa00d43837"><div class="ttname"><a href="namespacescran__aggregate.html#a8c5e32aa2efd50f80d02fcfa00d43837">scran_aggregate::aggregate_across_genes</a></div><div class="ttdeci">void aggregate_across_genes(const tatami::Matrix&lt; Data_, Index_ &gt; &amp;input, const std::vector&lt; std::tuple&lt; size_t, const Gene_ *, const Weight_ * &gt; &gt; &amp;gene_sets, const AggregateAcrossGenesBuffers&lt; Sum_ &gt; &amp;buffers, const AggregateAcrossGenesOptions &amp;options)</div><div class="ttdef"><b>Definition</b> aggregate_across_genes.hpp:269</div></div>
<div class="ttc" id="anamespacescran__aggregate_html_a8c5e32aa2efd50f80d02fcfa00d43837"><div class="ttname"><a href="namespacescran__aggregate.html#a8c5e32aa2efd50f80d02fcfa00d43837">scran_aggregate::aggregate_across_genes</a></div><div class="ttdeci">void aggregate_across_genes(const tatami::Matrix&lt; Data_, Index_ &gt; &amp;input, const std::vector&lt; std::tuple&lt; size_t, const Gene_ *, const Weight_ * &gt; &gt; &amp;gene_sets, const AggregateAcrossGenesBuffers&lt; Sum_ &gt; &amp;buffers, const AggregateAcrossGenesOptions &amp;options)</div><div class="ttdef"><b>Definition</b> aggregate_across_genes.hpp:284</div></div>
<div class="ttc" id="astructscran__aggregate_1_1AggregateAcrossGenesOptions_html"><div class="ttname"><a href="structscran__aggregate_1_1AggregateAcrossGenesOptions.html">scran_aggregate::AggregateAcrossGenesOptions</a></div><div class="ttdoc">Options for aggregate_across_genes().</div><div class="ttdef"><b>Definition</b> aggregate_across_genes.hpp:21</div></div>
</div><!-- fragment --><p>Check out the <a href="https://libscran.github.io/scran_aggregate">reference documentation</a> for more details.</p>
<h1>Building projects</h1>
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70 changes: 34 additions & 36 deletions docs/scran__aggregate_8hpp.html
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