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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-20T15:59:09","documenter_version":"1.4.1"}}
{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-20T19:17:03","documenter_version":"1.4.1"}}
2 changes: 1 addition & 1 deletion dev/datamatrices/index.html
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35340 │ P2_L5_TTTGTTGTCCGTGCGA P2 L5_TTTGTTGTCCGTGCGA
<span class="sgr36"> 35333 rows omitted</span></code></pre><h2 id="IDs"><a class="docs-heading-anchor" href="#IDs">IDs</a><a id="IDs-1"></a><a class="docs-heading-anchor-permalink" href="#IDs" title="Permalink"></a></h2><p>Each variable and each observation must have a unique ID, that is, each row in the <code>DataFrame</code> should be unique if we consider the ID columns only. As seen above, the ID columns are underlined when displaying a DataMatrix. We can also access them directly:</p><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; data.var_id_cols</code><code class="nohighlight hljs ansi" style="display:block;">ERROR: type DataMatrix has no field var_id_cols</code></pre><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; data.obs_id_cols</code><code class="nohighlight hljs ansi" style="display:block;">ERROR: type DataMatrix has no field obs_id_cols</code></pre><p>Most of the time, IDs are handled automatically by SingleCellProjections.jl. Sometimes, you need to make sure IDs are unique when loading or merging data matrices. In particular, when loading a <code>DataMatrix</code> that should be projected onto another <code>DataMatrix</code>, the user must ensure that relevant IDs are matching.</p><h2 id="Matrix"><a class="docs-heading-anchor" href="#Matrix">Matrix</a><a id="Matrix-1"></a><a class="docs-heading-anchor-permalink" href="#Matrix" title="Permalink"></a></h2><p>The matrix can be accessed by <code>data.matrix</code>. Depending on the stage of analysis, different kinds of matrices (or matrix-like objects) are used. Most of this complexity is hidden from the user, but internally SingleCellProjections.jl depends on this functionality to be fast and to reduce memory usage.</p><div class="admonition is-warning"><header class="admonition-header">Read-only</header><div class="admonition-body"><p>SingleCellProjections.jl will reuse matrices when possible, in order to reduce memory usage. E.g. <a href="../interface/#SingleCellProjections.normalize_matrix-Tuple{DataMatrix, SingleCellProjections.DesignMatrix}"><code>normalize_matrix</code></a> will reuse and extend the Matrix Expression of the source <code>DataMatrix</code>, without creating a copy of the actual data. When matrices are reused/copied is considered an implementation detail, and can change at any time. Users of SingleCellProjections.jl should thus consider the matrices to be &quot;read-only&quot;. This should rarely present problems in practice.</p></div></div><p>Roughly, the matrix types used at different stages are:</p><ol><li>Counts - <a href="https://docs.julialang.org/en/v1/stdlib/SparseArrays/"><code>SparseMatrixCSC</code></a></li><li>Transformed and normalized data - <a href="../matrixexpressions/#Matrix-Expressions">Matrix Expressions</a></li><li>SVD (PCA) result - <a href="https://docs.julialang.org/en/v1/stdlib/LinearAlgebra/#LinearAlgebra.SVD"><code>SVD</code></a></li><li>ForceLayout/UMAP/t-SNE result - <code>Matrix{Float64}</code></li></ol></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../tutorial/">« Tutorial</a><a class="docs-footer-nextpage" href="../matrixexpressions/">Matrix Expressions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Thursday 20 June 2024 15:59">Thursday 20 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
<span class="sgr36"> 35333 rows omitted</span></code></pre><h2 id="IDs"><a class="docs-heading-anchor" href="#IDs">IDs</a><a id="IDs-1"></a><a class="docs-heading-anchor-permalink" href="#IDs" title="Permalink"></a></h2><p>Each variable and each observation must have a unique ID, that is, each row in the <code>DataFrame</code> should be unique if we consider the ID columns only. As seen above, the ID columns are underlined when displaying a DataMatrix. We can also access them directly:</p><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; data.var_id_cols</code><code class="nohighlight hljs ansi" style="display:block;">ERROR: type DataMatrix has no field var_id_cols</code></pre><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; data.obs_id_cols</code><code class="nohighlight hljs ansi" style="display:block;">ERROR: type DataMatrix has no field obs_id_cols</code></pre><p>Most of the time, IDs are handled automatically by SingleCellProjections.jl. Sometimes, you need to make sure IDs are unique when loading or merging data matrices. In particular, when loading a <code>DataMatrix</code> that should be projected onto another <code>DataMatrix</code>, the user must ensure that relevant IDs are matching.</p><h2 id="Matrix"><a class="docs-heading-anchor" href="#Matrix">Matrix</a><a id="Matrix-1"></a><a class="docs-heading-anchor-permalink" href="#Matrix" title="Permalink"></a></h2><p>The matrix can be accessed by <code>data.matrix</code>. Depending on the stage of analysis, different kinds of matrices (or matrix-like objects) are used. Most of this complexity is hidden from the user, but internally SingleCellProjections.jl depends on this functionality to be fast and to reduce memory usage.</p><div class="admonition is-warning"><header class="admonition-header">Read-only</header><div class="admonition-body"><p>SingleCellProjections.jl will reuse matrices when possible, in order to reduce memory usage. E.g. <a href="../interface/#SingleCellProjections.normalize_matrix-Tuple{DataMatrix, SingleCellProjections.DesignMatrix}"><code>normalize_matrix</code></a> will reuse and extend the Matrix Expression of the source <code>DataMatrix</code>, without creating a copy of the actual data. When matrices are reused/copied is considered an implementation detail, and can change at any time. Users of SingleCellProjections.jl should thus consider the matrices to be &quot;read-only&quot;. This should rarely present problems in practice.</p></div></div><p>Roughly, the matrix types used at different stages are:</p><ol><li>Counts - <a href="https://docs.julialang.org/en/v1/stdlib/SparseArrays/"><code>SparseMatrixCSC</code></a></li><li>Transformed and normalized data - <a href="../matrixexpressions/#Matrix-Expressions">Matrix Expressions</a></li><li>SVD (PCA) result - <a href="https://docs.julialang.org/en/v1/stdlib/LinearAlgebra/#LinearAlgebra.SVD"><code>SVD</code></a></li><li>ForceLayout/UMAP/t-SNE result - <code>Matrix{Float64}</code></li></ol></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../tutorial/">« Tutorial</a><a class="docs-footer-nextpage" href="../matrixexpressions/">Matrix Expressions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Thursday 20 June 2024 19:17">Thursday 20 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · SingleCellProjections.jl</title><meta name="title" content="Home · SingleCellProjections.jl"/><meta property="og:title" content="Home · SingleCellProjections.jl"/><meta property="twitter:title" content="Home · SingleCellProjections.jl"/><meta name="description" content="Documentation for SingleCellProjections.jl."/><meta property="og:description" content="Documentation for SingleCellProjections.jl."/><meta property="twitter:description" content="Documentation for SingleCellProjections.jl."/><meta property="og:url" content="https://BioJulia.github.io/SingleCellProjections.jl/"/><meta property="twitter:url" content="https://BioJulia.github.io/SingleCellProjections.jl/"/><link rel="canonical" href="https://BioJulia.github.io/SingleCellProjections.jl/"/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>SingleCellProjections.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li><li><a class="tocitem" href="#Threading"><span>Threading</span></a></li></ul></li><li><a class="tocitem" href="tutorial/">Tutorial</a></li><li><a class="tocitem" href="datamatrices/">Data Matrices</a></li><li><a class="tocitem" href="matrixexpressions/">Matrix Expressions</a></li><li><a class="tocitem" href="interface/">Interface</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/BioJulia/SingleCellProjections.jl/blob/main/docs/src/index.md#" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="SingleCellProjections"><a class="docs-heading-anchor" href="#SingleCellProjections">SingleCellProjections</a><a id="SingleCellProjections-1"></a><a class="docs-heading-anchor-permalink" href="#SingleCellProjections" title="Permalink"></a></h1><p><a href="https://github.com/rasmushenningsson/SingleCellProjections.jl">SingleCellProjections.jl</a> is an easy to use and powerful package for analysis of Single Cell Expression data in Julia. It is faster and uses less memory than existing solutions since the data is internally represented as expressions of sparse and low rank matrices, instead of storing huge dense matrices. In particular, it efficiently performs PCA (Principal Component Analysis), a natural starting point for downstream analysis, and supports both standard workflows and projections onto a base data set.</p><p>Source code: <a href="https://github.com/rasmushenningsson/SingleCellProjections.jl">SingleCellProjections.jl</a>.</p><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>Install SingleCellProjections.jl by running the following commands in Julia:</p><pre><code class="language-julia hljs">using Pkg
Pkg.add(&quot;SingleCellProjections&quot;)</code></pre><h2 id="Threading"><a class="docs-heading-anchor" href="#Threading">Threading</a><a id="Threading-1"></a><a class="docs-heading-anchor-permalink" href="#Threading" title="Permalink"></a></h2><p>SingleCellProjections.jl relies heavily on threading. Please make sure to <a href="https://docs.julialang.org/en/v1/manual/multi-threading/">enable threading in Julia</a> to dramatically improve computation speed.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorial/">Tutorial »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Thursday 20 June 2024 15:59">Thursday 20 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
Pkg.add(&quot;SingleCellProjections&quot;)</code></pre><h2 id="Threading"><a class="docs-heading-anchor" href="#Threading">Threading</a><a id="Threading-1"></a><a class="docs-heading-anchor-permalink" href="#Threading" title="Permalink"></a></h2><p>SingleCellProjections.jl relies heavily on threading. Please make sure to <a href="https://docs.julialang.org/en/v1/manual/multi-threading/">enable threading in Julia</a> to dramatically improve computation speed.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorial/">Tutorial »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Thursday 20 June 2024 19:17">Thursday 20 June 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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