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malariagen · Dec 3, 2024 · ee15729 · ee15729
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diff --git a/latest/.doctrees/Af1.doctree b/latest/.doctrees/Af1.doctree
diff --git a/latest/.doctrees/Ag3.doctree b/latest/.doctrees/Ag3.doctree
diff --git a/latest/.doctrees/environment.pickle b/latest/.doctrees/environment.pickle
diff --git a/latest/.doctrees/generated/malariagen_data.af1.Af1.haplotypes_frequencies.doctree b/latest/.doctrees/generated/malariagen_data.af1.Af1.haplotypes_frequencies.doctree
diff --git a/latest/.doctrees/generated/malariagen_data.af1.Af1.haplotypes_frequencies_advanced.doctree b/latest/.doctrees/generated/malariagen_data.af1.Af1.haplotypes_frequencies_advanced.doctree
diff --git a/latest/.doctrees/generated/malariagen_data.ag3.Ag3.haplotypes_frequencies.doctree b/latest/.doctrees/generated/malariagen_data.ag3.Ag3.haplotypes_frequencies.doctree
diff --git a/latest/.doctrees/generated/malariagen_data.ag3.Ag3.haplotypes_frequencies_advanced.doctree b/latest/.doctrees/generated/malariagen_data.ag3.Ag3.haplotypes_frequencies_advanced.doctree
diff --git a/latest/Af1.html b/latest/Af1.html
@@ -572,6 +572,12 @@ <h2>SNP and CNV frequency analysis<a class="headerlink" href="#snp-and-cnv-frequ
 <tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.af1.Af1.gene_cnv_frequencies_advanced.html#malariagen_data.af1.Af1.gene_cnv_frequencies_advanced" title="malariagen_data.af1.Af1.gene_cnv_frequencies_advanced"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gene_cnv_frequencies_advanced</span></code></a>(region, ...[, ...])</p></td>
 <td><p>Group samples by taxon, area (space) and period (time), then compute gene CNV counts and frequencies.</p></td>
 </tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.af1.Af1.haplotypes_frequencies.html#malariagen_data.af1.Af1.haplotypes_frequencies" title="malariagen_data.af1.Af1.haplotypes_frequencies"><code class="xref py py-obj docutils literal notranslate"><span class="pre">haplotypes_frequencies</span></code></a>(region, cohorts[, ...])</p></td>
+<td><p>Compute haplotype frequencies for a region.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.af1.Af1.haplotypes_frequencies_advanced.html#malariagen_data.af1.Af1.haplotypes_frequencies_advanced" title="malariagen_data.af1.Af1.haplotypes_frequencies_advanced"><code class="xref py py-obj docutils literal notranslate"><span class="pre">haplotypes_frequencies_advanced</span></code></a>(region, ...)</p></td>
+<td><p>Group samples by taxon, area (space) and period (time), then compute haplotype frequencies.</p></td>
+</tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.af1.Af1.plot_frequencies_heatmap.html#malariagen_data.af1.Af1.plot_frequencies_heatmap" title="malariagen_data.af1.Af1.plot_frequencies_heatmap"><code class="xref py py-obj docutils literal notranslate"><span class="pre">plot_frequencies_heatmap</span></code></a>(df[, index, ...])</p></td>
 <td><p>Plot a heatmap from a pandas DataFrame of frequencies, e.g., output from <cite>snp_allele_frequencies()</cite> or <cite>gene_cnv_frequencies()</cite>.</p></td>
 </tr>

diff --git a/latest/Ag3.html b/latest/Ag3.html
@@ -597,6 +597,12 @@ <h2>SNP and CNV frequency analysis<a class="headerlink" href="#snp-and-cnv-frequ
 <tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.gene_cnv_frequencies_advanced.html#malariagen_data.ag3.Ag3.gene_cnv_frequencies_advanced" title="malariagen_data.ag3.Ag3.gene_cnv_frequencies_advanced"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gene_cnv_frequencies_advanced</span></code></a>(region, ...[, ...])</p></td>
 <td><p>Group samples by taxon, area (space) and period (time), then compute gene CNV counts and frequencies.</p></td>
 </tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.haplotypes_frequencies.html#malariagen_data.ag3.Ag3.haplotypes_frequencies" title="malariagen_data.ag3.Ag3.haplotypes_frequencies"><code class="xref py py-obj docutils literal notranslate"><span class="pre">haplotypes_frequencies</span></code></a>(region, cohorts[, ...])</p></td>
+<td><p>Compute haplotype frequencies for a region.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.haplotypes_frequencies_advanced.html#malariagen_data.ag3.Ag3.haplotypes_frequencies_advanced" title="malariagen_data.ag3.Ag3.haplotypes_frequencies_advanced"><code class="xref py py-obj docutils literal notranslate"><span class="pre">haplotypes_frequencies_advanced</span></code></a>(region, ...)</p></td>
+<td><p>Group samples by taxon, area (space) and period (time), then compute haplotype frequencies.</p></td>
+</tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/malariagen_data.ag3.Ag3.plot_frequencies_heatmap.html#malariagen_data.ag3.Ag3.plot_frequencies_heatmap" title="malariagen_data.ag3.Ag3.plot_frequencies_heatmap"><code class="xref py py-obj docutils literal notranslate"><span class="pre">plot_frequencies_heatmap</span></code></a>(df[, index, ...])</p></td>
 <td><p>Plot a heatmap from a pandas DataFrame of frequencies, e.g., output from <cite>snp_allele_frequencies()</cite> or <cite>gene_cnv_frequencies()</cite>.</p></td>
 </tr>

diff --git a/latest/_sources/Af1.rst.txt b/latest/_sources/Af1.rst.txt
@@ -115,6 +115,8 @@ SNP and CNV frequency analysis
     aa_allele_frequencies_advanced
     gene_cnv_frequencies
     gene_cnv_frequencies_advanced
+    haplotypes_frequencies
+    haplotypes_frequencies_advanced
     plot_frequencies_heatmap
     plot_frequencies_time_series
     plot_frequencies_interactive_map

diff --git a/latest/_sources/Ag3.rst.txt b/latest/_sources/Ag3.rst.txt
@@ -125,6 +125,8 @@ SNP and CNV frequency analysis
     aa_allele_frequencies_advanced
     gene_cnv_frequencies
     gene_cnv_frequencies_advanced
+    haplotypes_frequencies
+    haplotypes_frequencies_advanced
     plot_frequencies_heatmap
     plot_frequencies_time_series
     plot_frequencies_interactive_map

diff --git a/latest/_sources/generated/malariagen_data.af1.Af1.haplotypes_frequencies.rst.txt b/latest/_sources/generated/malariagen_data.af1.Af1.haplotypes_frequencies.rst.txt
@@ -0,0 +1,6 @@
+malariagen\_data.af1.Af1.haplotypes\_frequencies
+================================================
+
+.. currentmodule:: malariagen_data.af1
+
+.. automethod:: Af1.haplotypes_frequencies
diff --git a/...urces/generated/malariagen_data.af1.Af1.haplotypes_frequencies_advanced.rst.txt b/...urces/generated/malariagen_data.af1.Af1.haplotypes_frequencies_advanced.rst.txt
@@ -0,0 +1,6 @@
+malariagen\_data.af1.Af1.haplotypes\_frequencies\_advanced
+==========================================================
+
+.. currentmodule:: malariagen_data.af1
+
+.. automethod:: Af1.haplotypes_frequencies_advanced
diff --git a/latest/_sources/generated/malariagen_data.ag3.Ag3.haplotypes_frequencies.rst.txt b/latest/_sources/generated/malariagen_data.ag3.Ag3.haplotypes_frequencies.rst.txt
@@ -0,0 +1,6 @@
+malariagen\_data.ag3.Ag3.haplotypes\_frequencies
+================================================
+
+.. currentmodule:: malariagen_data.ag3
+
+.. automethod:: Ag3.haplotypes_frequencies
diff --git a/...urces/generated/malariagen_data.ag3.Ag3.haplotypes_frequencies_advanced.rst.txt b/...urces/generated/malariagen_data.ag3.Ag3.haplotypes_frequencies_advanced.rst.txt
@@ -0,0 +1,6 @@
+malariagen\_data.ag3.Ag3.haplotypes\_frequencies\_advanced
+==========================================================
+
+.. currentmodule:: malariagen_data.ag3
+
+.. automethod:: Ag3.haplotypes_frequencies_advanced