Docs files for scanpy labs 02-06

docs/labs/scanpy/scanpy_02_dimred.html

@@ -199,7 +199,7 @@ <h1 class="title"><i class="fa-brands fa-hubspot" aria-label="hubspot"></i> Dime
       <div>
       <div class="quarto-title-meta-heading">Published</div>
       <div class="quarto-title-meta-contents">
-        <p class="date">16-Jan-2024</p>
+        <p class="date">19-Jan-2024</p>
       </div>
     </div>
 
@@ -282,10 +282,10 @@ <h2 data-number="1" class="anchored" data-anchor-id="meta-dimred_prep"><span cla
 <span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>adata <span class="op">=</span> sc.read_h5ad(path_file)</span>
 <span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a>adata</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-display" data-execution_count="2">
-<pre><code>AnnData object with n_obs × n_vars = 5725 × 18830
+<pre><code>AnnData object with n_obs × n_vars = 7222 × 19468
     obs: 'type', 'sample', 'batch', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'pct_counts_ribo', 'total_counts_hb', 'pct_counts_hb', 'percent_mt2', 'n_counts', 'n_genes', 'percent_chrY', 'XIST-counts', 'S_score', 'G2M_score', 'phase', 'doublet_scores', 'predicted_doublets', 'doublet_info'
     var: 'gene_ids', 'feature_types', 'genome', 'mt', 'ribo', 'hb', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts', 'n_cells'
-    uns: 'doublet_info_colors', 'hvg', 'log1p', 'neighbors', 'pca', 'sample_colors', 'umap'
+    uns: 'doublet_info_colors', 'hvg', 'log1p', 'neighbors', 'pca', 'phase_colors', 'sample_colors', 'umap'
     obsm: 'X_pca', 'X_umap'
     obsp: 'connectivities', 'distances'</code></pre>
 </div>
@@ -309,10 +309,10 @@ <h2 data-number="1" class="anchored" data-anchor-id="meta-dimred_prep"><span cla
 WARNING: adata.X seems to be already log-transformed.</code></pre>
 </div>
 <div class="cell-output cell-output-display" data-execution_count="3">
-<pre><code>AnnData object with n_obs × n_vars = 5725 × 18830
+<pre><code>AnnData object with n_obs × n_vars = 7222 × 19468
     obs: 'type', 'sample', 'batch', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'pct_counts_ribo', 'total_counts_hb', 'pct_counts_hb', 'percent_mt2', 'n_counts', 'n_genes', 'percent_chrY', 'XIST-counts', 'S_score', 'G2M_score', 'phase', 'doublet_scores', 'predicted_doublets', 'doublet_info'
     var: 'gene_ids', 'feature_types', 'genome', 'mt', 'ribo', 'hb', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts', 'n_cells'
-    uns: 'doublet_info_colors', 'hvg', 'log1p', 'neighbors', 'pca', 'sample_colors', 'umap'
+    uns: 'doublet_info_colors', 'hvg', 'log1p', 'neighbors', 'pca', 'phase_colors', 'sample_colors', 'umap'
     obsm: 'X_pca', 'X_umap'
     obsp: 'connectivities', 'distances'</code></pre>
 </div>
@@ -339,7 +339,7 @@ <h2 data-number="2" class="anchored" data-anchor-id="meta-dimred_fs"><span class
     'means', float vector (adata.var)
     'dispersions', float vector (adata.var)
     'dispersions_norm', float vector (adata.var)
-Highly variable genes: 2727</code></pre>
+Highly variable genes: 2626</code></pre>
 </div>
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 <div class="quarto-figure quarto-figure-left">
@@ -365,7 +365,7 @@ <h2 data-number="3" class="anchored" data-anchor-id="meta-dimred_zs"><span class
 <div class="cell-output cell-output-stdout">
 <pre><code>regressing out ['total_counts', 'pct_counts_mt']
     sparse input is densified and may lead to high memory use
-    finished (0:00:37)</code></pre>
+    finished (0:00:46)</code></pre>
 </div>
 </div>
 </section>
@@ -476,7 +476,7 @@ <h2 data-number="5" class="anchored" data-anchor-id="meta-dimred_tsne"><span cla
     using 'X_pca' with n_pcs = 30
     using sklearn.manifold.TSNE
     finished: added
-    'X_tsne', tSNE coordinates (adata.obsm) (0:00:10)</code></pre>
+    'X_tsne', tSNE coordinates (adata.obsm) (0:00:13)</code></pre>
 </div>
 </div>
 <p>We can now plot the tSNE colored per dataset. We can clearly see the effect of batches present in the dataset.</p>
@@ -511,7 +511,7 @@ <h2 data-number="6" class="anchored" data-anchor-id="meta-dimred_umap"><span cla
 <div class="cell-output cell-output-stdout">
 <pre><code>computing UMAP
     finished: added
-    'X_umap', UMAP coordinates (adata.obsm) (0:00:09)</code></pre>
+    'X_umap', UMAP coordinates (adata.obsm) (0:00:12)</code></pre>
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@@ -539,7 +539,7 @@ <h2 data-number="6" class="anchored" data-anchor-id="meta-dimred_umap"><span cla
 <div class="cell-output cell-output-stdout">
 <pre><code>computing UMAP
     finished: added
-    'X_umap', UMAP coordinates (adata.obsm) (0:00:10)</code></pre>
+    'X_umap', UMAP coordinates (adata.obsm) (0:00:13)</code></pre>
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 <div class="quarto-figure quarto-figure-left">
@@ -678,12 +678,22 @@ <h2 data-number="8" class="anchored" data-anchor-id="meta-dimred_save"><span cla
 <div class="cell" data-execution_count="19">
 <div class="sourceCode cell-code" id="cb30"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb30-1"><a href="#cb30-1" aria-hidden="true" tabindex="-1"></a>adata.write_h5ad(<span class="st">'data/covid/results/scanpy_covid_qc_dr.h5ad'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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+<p>Just a reminder, you need to keep in mind what you have in the X matrix. After these operations you have an X matrix with only variable genes, that are normalized, logtransformed and scaled.</p>
+<p>We stored the expression of all genes in <code>raw.X</code> after doing lognormalization so that matrix is a sparse matrix with logtransformed values.</p>
 <div class="cell" data-execution_count="20">
 <div class="sourceCode cell-code" id="cb31"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb31-1"><a href="#cb31-1" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(adata.X.shape)</span>
-<span id="cb31-2"><a href="#cb31-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(adata.raw.X.shape)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb31-2"><a href="#cb31-2" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(adata.raw.X.shape)</span>
+<span id="cb31-3"><a href="#cb31-3" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb31-4"><a href="#cb31-4" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(adata.X[:<span class="dv">3</span>,:<span class="dv">3</span>])</span>
+<span id="cb31-5"><a href="#cb31-5" aria-hidden="true" tabindex="-1"></a><span class="bu">print</span>(adata.raw.X[:<span class="dv">10</span>,:<span class="dv">10</span>])</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
-<pre><code>(5725, 2727)
-(5725, 18830)</code></pre>
+<pre><code>(7222, 2626)
+(7222, 19468)
+[[-0.16998859 -0.06050171 -0.08070081]
+ [-0.19315341 -0.09975121 -0.31379319]
+ [-0.2051203  -0.11680799 -0.43194618]]
+  (1, 4)    0.7825693876867097
+  (8, 7)    1.1311041336746985</code></pre>
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 </div>
 </section>
@@ -815,9 +825,9 @@ <h2 data-number="9" class="anchored" data-anchor-id="meta-session"><span class="
 notebook            6.5.4
 -----
 Python 3.10.11 | packaged by conda-forge | (main, May 10 2023, 18:58:44) [GCC 11.3.0]
-Linux-6.5.11-linuxkit-x86_64-with-glibc2.35
+Linux-6.4.16-linuxkit-x86_64-with-glibc2.35
 -----
-Session information updated at 2024-01-16 23:19</code></pre>
+Session information updated at 2024-01-19 14:53</code></pre>
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 </details>
@@ -1069,7 +1079,7 @@ <h2 data-number="9" class="anchored" data-anchor-id="meta-session"><span class="
     <div class="nav-footer-right">Published with <a href="https://quarto.org/">Quarto</a> v1.3.450</div>
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-<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","selector":".lightbox","descPosition":"bottom","loop":true,"openEffect":"zoom"});</script>
+<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","selector":".lightbox","openEffect":"zoom","loop":true,"descPosition":"bottom"});</script>