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125 lines
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HTML
125 lines
5.1 KiB
HTML
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<a href="/" class="btn">Quick start</a><br>
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<a href="/posts/methods" class="btn"><b>Methods</b></a><br>
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<section>
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<h1 id="methods">Methods</h1>
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<h2 id="data-structure-anndata-fields-used-for-visualization">Data structure: <em>anndata</em> fields used for visualization</h2>
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<h3 id="expression-data">Expression data</h3>
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<p>Gene expression values are pulled from <code class="highlighter-rouge">anndata.X</code>. These feed into the histograms, scatterplot, colorscale, and differential expression calculations. We’re <a href="https://github.com/chanzuckerberg/cellxgene/issues/689">working on ways</a> to incorporate <code class="highlighter-rouge">anndata.raw</code> and other <code class="highlighter-rouge">anndata.layers</code>!</p>
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<h3 id="metadata">Metadata</h3>
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<p>Categorical (e.g., cluster labels) and continuous (e.g., pseudotime) metadata are pulled from <code class="highlighter-rouge">anndata.obs</code>. Any column added here will be available for visualization in cellxgene. You can also <a href="annotations">create new categorical annotations</a> within the application.</p>
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<h3 id="embeddings">Embeddings</h3>
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<p>cellxgene looks for embeddings (e.g., tSNE, UMAP, PCA, spatial coordinates) in <code class="highlighter-rouge">anndata.obsm</code>. These fields must follow the scanpy convention of starting with <code class="highlighter-rouge">X_</code>, e.g., <code class="highlighter-rouge">anndata.obsm['X_umap']</code>. If an embedding has more than two components, the first two will be used for visualization.</p>
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<h2 id="differential-expression">Differential expression</h2>
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<p>We’re actively working on how to improve differential expression within the app.</p>
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<p>Currently, we use a <a href="https://en.wikipedia.org/wiki/Welch%27s_t-test">Welch’s <em>t</em>-test</a> implementation, including the same variance overestimation correction as used in <code class="highlighter-rouge">scanpy</code>. We sort the <code class="highlighter-rouge">tscore</code> to identify the top 15 genes, and then filter to remove any that fall below a cutoff log fold change value, which can help remove spurious test results. The default threshold is <code class="highlighter-rouge">0.01</code> and can be changed using the option <code class="highlighter-rouge">--diffexp-lfc-cutoff</code>.</p>
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</section>
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<footer>
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<p>This project is maintained by <a href="https://github.com/chanzuckerberg">chanzuckerberg</a></p>
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