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Add more contracts.
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@orenbenkiki
orenbenkiki committed Jun 20, 2024
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2 changes: 1 addition & 1 deletion docs/v0.1.0/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-20T17:22:53","documenter_version":"1.4.1"}}
{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-20T17:56:23","documenter_version":"1.4.1"}}
12 changes: 6 additions & 6 deletions docs/v0.1.0/boxes.html
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Expand Up @@ -249,7 +249,7 @@ <h1 id="Boxes">
</p>
<p>
<strong>metacell @ total_UMIs
</strong>::AbstractFloat (required): The total number of UMIs used to estimate the fraction of all the genes in each metacell.
</strong>::Unsigned (required): The total number of UMIs used to estimate the fraction of all the genes in each metacell.
</p>
<p>
<strong>Matrices
Expand All @@ -261,7 +261,7 @@ <h1 id="Boxes">
</p>
<p>
<strong>gene, metacell @ total_UMIs
</strong>::AbstractFloat (required): The total number of UMIs used to estimate the fraction of each gene in each metacell.
</strong>::Unsigned (required): The total number of UMIs used to estimate the fraction of each gene in each metacell.
</p>
<p>
<strong>Outputs
Expand All @@ -285,11 +285,11 @@ <h1 id="Boxes">
</p>
<p>
<strong>metacell @ box
</strong>::AbstractFloat (guaranteed): The unique box each metacell belongs to.
</strong>::AbstractString (guaranteed): The unique box each metacell belongs to.
</p>
<p>
<strong>box @ neighborhood.main
</strong>::AbstractFloat (guaranteed): The unique main neighborhood of each box.
</strong>::AbstractString (guaranteed): The unique main neighborhood of each box.
</p>
<p>
<strong>neighborhood @ span
Expand All @@ -301,15 +301,15 @@ <h1 id="Boxes">
</p>
<p>
<strong>gene, neighborhood @ is_correlated
</strong>::AbstractFloat (guaranteed): Which genes are correlated in each neighborhood.
</strong>::Bool (guaranteed): Which genes are correlated in each neighborhood.
</p>
<p>
<strong>box, box @ distance
</strong>::AbstractFloat (guaranteed): The distance (fold factor) between the most different metacell genes between the boxes.
</p>
<p>
<strong>box, neighborhood @ is_member
</strong>::AbstractFloat (guaranteed): A mask of the member boxes of each neighborhood.
</strong>::Bool (guaranteed): A mask of the member boxes of each neighborhood.
</p>
</div>
</section>
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168 changes: 168 additions & 0 deletions docs/v0.1.0/contracts.html
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Expand Up @@ -514,6 +514,28 @@ <h2 id="Vectors">
<header>
<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
</a>
<a class="docstring-binding" id="Metacells.Contracts.metacell_type_vector" href="#Metacells.Contracts.metacell_type_vector">
<code>Metacells.Contracts.metacell_type_vector
</code>
</a> —
<span class="docstring-category">Function
</span>
</header>
<section>
<div>
<pre>
<code class="language-julia hljs">function metacell_type_vector(expectation::ContractExpectation)::Pair{VectorKey, DataSpecification}
</code>
</pre>
<p>The type each metacell belongs to.
</p>
</div>
</section>
</article>
<article class="docstring">
<header>
<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
</a>
<a class="docstring-binding" id="Metacells.Contracts.box_main_neighborhood_vector" href="#Metacells.Contracts.box_main_neighborhood_vector">
<code>Metacells.Contracts.box_main_neighborhood_vector
</code>
Expand All @@ -536,6 +558,50 @@ <h2 id="Vectors">
<header>
<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
</a>
<a class="docstring-binding" id="Metacells.Contracts.box_total_UMIs_vector" href="#Metacells.Contracts.box_total_UMIs_vector">
<code>Metacells.Contracts.box_total_UMIs_vector
</code>
</a> —
<span class="docstring-category">Function
</span>
</header>
<section>
<div>
<pre>
<code class="language-julia hljs">function box_total_UMIs_vector(expectation::ContractExpectation)::Pair{VectorKey, DataSpecification}
</code>
</pre>
<p>The unique main neighborhood of each box. Ideally, each box is the center of its own main neighborhood, and also belongs to overlapping neighborhood of some other nearby boxes. However, where the manifold is sparsely sampled, a few nearby boxes may share the same main neighborhood. If the samples are sufficiently sparse, the main neighborhood may include only just the single box (which itself may include just a single metacell).
</p>
</div>
</section>
</article>
<article class="docstring">
<header>
<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
</a>
<a class="docstring-binding" id="Metacells.Contracts.box_type_vector" href="#Metacells.Contracts.box_type_vector">
<code>Metacells.Contracts.box_type_vector
</code>
</a> —
<span class="docstring-category">Function
</span>
</header>
<section>
<div>
<pre>
<code class="language-julia hljs">function box_type_vector(expectation::ContractExpectation)::Pair{VectorKey, DataSpecification}
</code>
</pre>
<p>The type each box belongs to.
</p>
</div>
</section>
</article>
<article class="docstring">
<header>
<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
</a>
<a class="docstring-binding" id="Metacells.Contracts.neighborhood_span_vector" href="#Metacells.Contracts.neighborhood_span_vector">
<code>Metacells.Contracts.neighborhood_span_vector
</code>
Expand All @@ -554,6 +620,28 @@ <h2 id="Vectors">
</div>
</section>
</article>
<article class="docstring">
<header>
<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
</a>
<a class="docstring-binding" id="Metacells.Contracts.type_color_vector" href="#Metacells.Contracts.type_color_vector">
<code>Metacells.Contracts.type_color_vector
</code>
</a> —
<span class="docstring-category">Function
</span>
</header>
<section>
<div>
<pre>
<code class="language-julia hljs">function type_color_vector(expectation::ContractExpectation)::Pair{VectorKey, DataSpecification}
</code>
</pre>
<p>A unique color for each type for graphs.
</p>
</div>
</section>
</article>
<h2 id="Matrices">
<a class="docs-heading-anchor" href="#Matrices">Matrices
</a>
Expand Down Expand Up @@ -654,6 +742,50 @@ <h2 id="Matrices">
<header>
<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
</a>
<a class="docstring-binding" id="Metacells.Contracts.gene_box_fraction_matrix" href="#Metacells.Contracts.gene_box_fraction_matrix">
<code>Metacells.Contracts.gene_box_fraction_matrix
</code>
</a> —
<span class="docstring-category">Function
</span>
</header>
<section>
<div>
<pre>
<code class="language-julia hljs">function gene_box_fraction_matrix(expectation::ContractExpectation)::Pair{MatrixKey, DataSpecification}
</code>
</pre>
<p>The estimated fraction of the UMIs of each gene in each box. Each box is a sample of the manifold, representing a real biological state, which is different from the state of any other box.
</p>
</div>
</section>
</article>
<article class="docstring">
<header>
<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
</a>
<a class="docstring-binding" id="Metacells.Contracts.gene_box_total_UMIs_matrix" href="#Metacells.Contracts.gene_box_total_UMIs_matrix">
<code>Metacells.Contracts.gene_box_total_UMIs_matrix
</code>
</a> —
<span class="docstring-category">Function
</span>
</header>
<section>
<div>
<pre>
<code class="language-julia hljs">function gene_box_total_UMIs_matrix(expectation::ContractExpectation)::Pair{MatrixKey, DataSpecification}
</code>
</pre>
<p>The total number of UMIs used to estimate the fraction of each gene in each box. This is used to estimate the robustness of the estimate. When computing fold factors, we require the total number of UMIs (from both compared estimates) to be some minimum, and possibly adjust the fold factor according to some confidence level (assuming a multinomial sampling distribution).
</p>
</div>
</section>
</article>
<article class="docstring">
<header>
<a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring">
</a>
<a class="docstring-binding" id="Metacells.Contracts.box_neighborhood_is_member_matrix" href="#Metacells.Contracts.box_neighborhood_is_member_matrix">
<code>Metacells.Contracts.box_neighborhood_is_member_matrix
</code>
Expand Down Expand Up @@ -712,6 +844,18 @@ <h2 id="Index">
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.box_total_UMIs_vector">
<code>Metacells.Contracts.box_total_UMIs_vector
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.box_type_vector">
<code>Metacells.Contracts.box_type_vector
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.cell_axis">
<code>Metacells.Contracts.cell_axis
</code>
Expand All @@ -730,6 +874,18 @@ <h2 id="Index">
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.gene_box_fraction_matrix">
<code>Metacells.Contracts.gene_box_fraction_matrix
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.gene_box_total_UMIs_matrix">
<code>Metacells.Contracts.gene_box_total_UMIs_matrix
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.gene_divergence_vector">
<code>Metacells.Contracts.gene_divergence_vector
</code>
Expand Down Expand Up @@ -796,6 +952,12 @@ <h2 id="Index">
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.metacell_type_vector">
<code>Metacells.Contracts.metacell_type_vector
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.neighborhood_axis">
<code>Metacells.Contracts.neighborhood_axis
</code>
Expand All @@ -813,6 +975,12 @@ <h2 id="Index">
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.type_color_vector">
<code>Metacells.Contracts.type_color_vector
</code>
</a>
</li>
</ul>
</article>
<nav class="docs-footer">
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36 changes: 36 additions & 0 deletions docs/v0.1.0/index.html
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Expand Up @@ -246,6 +246,18 @@ <h1 id="Index">
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.box_total_UMIs_vector">
<code>Metacells.Contracts.box_total_UMIs_vector
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.box_type_vector">
<code>Metacells.Contracts.box_type_vector
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.cell_axis">
<code>Metacells.Contracts.cell_axis
</code>
Expand All @@ -264,6 +276,18 @@ <h1 id="Index">
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.gene_box_fraction_matrix">
<code>Metacells.Contracts.gene_box_fraction_matrix
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.gene_box_total_UMIs_matrix">
<code>Metacells.Contracts.gene_box_total_UMIs_matrix
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.gene_divergence_vector">
<code>Metacells.Contracts.gene_divergence_vector
</code>
Expand Down Expand Up @@ -330,6 +354,12 @@ <h1 id="Index">
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.metacell_type_vector">
<code>Metacells.Contracts.metacell_type_vector
</code>
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.neighborhood_axis">
<code>Metacells.Contracts.neighborhood_axis
</code>
Expand All @@ -348,6 +378,12 @@ <h1 id="Index">
</a>
</li>
<li>
<a href="contracts.html#Metacells.Contracts.type_color_vector">
<code>Metacells.Contracts.type_color_vector
</code>
</a>
</li>
<li>
<a href="identify_genes.html#Metacells.IdentifyGenes.compute_genes_divergence!">
<code>Metacells.IdentifyGenes.compute_genes_divergence!
</code>
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2 changes: 1 addition & 1 deletion docs/v0.1.0/search_index.js
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