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Add contracts.
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orenbenkiki committed Jun 20, 2024
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2 changes: 1 addition & 1 deletion deps/document.jl
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Expand Up @@ -46,7 +46,7 @@ makedocs(;
prettyurls = false,
size_threshold_warn = 200 * 2^10,
),
pages = ["index.md", "anndata_format.md", "identify_genes.md", "boxes.md"],
pages = ["index.md", "contracts.md", "identify_genes.md", "boxes.md", "anndata_format.md"],
)

if seen_problems
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2 changes: 1 addition & 1 deletion docs/v0.1.0/.documenter-siteinfo.json
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@@ -1 +1 @@
{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-17T13:39:41","documenter_version":"1.4.1"}}
{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-20T17:22:53","documenter_version":"1.4.1"}}
24 changes: 13 additions & 11 deletions docs/v0.1.0/anndata_format.html
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Expand Up @@ -52,6 +52,18 @@
<a class="tocitem" href="index.html">Metacells
</a>
</li>
<li>
<a class="tocitem" href="contracts.html">Contracts
</a>
</li>
<li>
<a class="tocitem" href="identify_genes.html">Identify Genes
</a>
</li>
<li>
<a class="tocitem" href="boxes.html">Boxes
</a>
</li>
<li class="is-active">
<a class="tocitem" href="anndata_format.html">AnnData Format
</a>
Expand All @@ -64,14 +76,6 @@
</li>
</ul>
</li>
<li>
<a class="tocitem" href="identify_genes.html">Identify Genes
</a>
</li>
<li>
<a class="tocitem" href="boxes.html">Boxes
</a>
</li>
</ul>
<div class="docs-version-selector field has-addons">
<div class="control">
Expand Down Expand Up @@ -555,9 +559,7 @@ <h2 id="Index">
</ul>
</article>
<nav class="docs-footer">
<a class="docs-footer-prevpage" href="index.html">« Metacells
</a>
<a class="docs-footer-nextpage" href="identify_genes.html">Identify Genes »
<a class="docs-footer-prevpage" href="boxes.html">« Boxes
</a>
<div class="flexbox-break">
</div>
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102 changes: 97 additions & 5 deletions docs/v0.1.0/boxes.html
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Expand Up @@ -53,7 +53,7 @@
</a>
</li>
<li>
<a class="tocitem" href="anndata_format.html">AnnData Format
<a class="tocitem" href="contracts.html">Contracts
</a>
</li>
<li>
Expand All @@ -72,6 +72,10 @@
</li>
</ul>
</li>
<li>
<a class="tocitem" href="anndata_format.html">AnnData Format
</a>
</li>
</ul>
<div class="docs-version-selector field has-addons">
<div class="control">
Expand Down Expand Up @@ -161,11 +165,11 @@ <h1 id="Boxes">
<code class="language-julia hljs">function compute_boxes!(
daf::DafWriter;
min_significant_gene_UMIs::Integer = 40,
gene_fraction_regularization::AbstractFloat = 1e-5,
gene_fraction_regularization::AbstractFloat = 1.0e-5,
fold_confidence::AbstractFloat = 0.9,
max_box_span::AbstractFloat = 2.0,
max_neighborhood_span::AbstractFloat = 2.0,
correlation_confidence::AbstractFloat = 0.99,
max_neighborhood_span::AbstractFloat = 0.01,
correlation_confidence::AbstractFloat = 0.9,
max_deviant_genes_fraction::AbstractFloat = 0.01,
overwrite::Bool = false,
)::Nothing
Expand Down Expand Up @@ -219,7 +223,93 @@ <h1 id="Boxes">
<code>overwrite
</code> is set, the results will replace any previously computed boxes and neighborhoods.
</p>
<p>CONTRACT
<p>
<strong>Inputs
</strong>
</p>
<p>
<strong>Axes
</strong>
</p>
<p>
<strong>gene
</strong> (required): Sequenced genes.
</p>
<p>
<strong>metacell
</strong> (required): Minimal-sized groups of cells for robust point estimates.
</p>
<p>
<strong>Vectors
</strong>
</p>
<p>
<strong>gene @ divergence
</strong>::AbstractFloat (required): Scale fold factors of each gene by multiplying with (1 - divergence) of the gene.
</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.
</p>
<p>
<strong>Matrices
</strong>
</p>
<p>
<strong>gene, metacell @ fraction
</strong>::AbstractFloat (required): The estimated fraction of the UMIs of each gene in each metacell.
</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.
</p>
<p>
<strong>Outputs
</strong>
</p>
<p>
<strong>Axes
</strong>
</p>
<p>
<strong>box
</strong> (guaranteed): Distinct groups of metacells with &quot;very close&quot; estimated cell state.
</p>
<p>
<strong>neighborhood
</strong> (guaranteed): Overlapping groups of boxes with &quot;close&quot; estimated cell states.
</p>
<p>
<strong>Vectors
</strong>
</p>
<p>
<strong>metacell @ box
</strong>::AbstractFloat (guaranteed): The unique box each metacell belongs to.
</p>
<p>
<strong>box @ neighborhood.main
</strong>::AbstractFloat (guaranteed): The unique main neighborhood of each box.
</p>
<p>
<strong>neighborhood @ span
</strong>::AbstractFloat (guaranteed): The span (fold factor) used to compute the neighborhood.
</p>
<p>
<strong>Matrices
</strong>
</p>
<p>
<strong>gene, neighborhood @ is_correlated
</strong>::AbstractFloat (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.
</p>
</div>
</section>
Expand Down Expand Up @@ -250,6 +340,8 @@ <h2 id="Index">
<nav class="docs-footer">
<a class="docs-footer-prevpage" href="identify_genes.html">« Identify Genes
</a>
<a class="docs-footer-nextpage" href="anndata_format.html">AnnData Format »
</a>
<div class="flexbox-break">
</div>
<p class="footer-message">Powered by
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