From 04785d178b20cd70876d99a81509fa24ea519403 Mon Sep 17 00:00:00 2001 From: Christophe Avenel Date: Wed, 29 Nov 2023 13:49:15 +0100 Subject: [PATCH] Update st_clustering.qmd Fix jinja variable in qmd file --- bin/st_clustering.qmd | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bin/st_clustering.qmd b/bin/st_clustering.qmd index cd64f70..8a6da8e 100644 --- a/bin/st_clustering.qmd +++ b/bin/st_clustering.qmd @@ -48,12 +48,13 @@ st_adata ## Manifold embedding and clustering based on transcriptional similarity -To uncover the underlying structure of the transcriptional landscape, we perform manifold embedding and clustering based on transcriptional similarity. Principal Component Analysis (PCA) is applied to reduce dimensionality, and UMAP (Uniform Manifold Approximation and Projection) is used for visualization. The Leiden algorithm is employed for clustering with a specified resolution of {{< var resolution >}}. +To uncover the underlying structure of the transcriptional landscape, we perform manifold embedding and clustering based on transcriptional similarity. Principal Component Analysis (PCA) is applied to reduce dimensionality, and UMAP (Uniform Manifold Approximation and Projection) is used for visualization. The Leiden algorithm is employed for clustering with a givent resolution. ```{python} sc.pp.pca(st_adata) sc.pp.neighbors(st_adata) sc.tl.umap(st_adata) +print (f"Resolution for Leiden clustering: {resolution}") sc.tl.leiden(st_adata, key_added="clusters", resolution=resolution) ```