From bf8daf422d9b3bb43b2ef4b20640c7baa868fbf8 Mon Sep 17 00:00:00 2001 From: Justin Hong Date: Thu, 6 Mar 2025 10:57:26 -0500 Subject: [PATCH] Update Decipher docs (#3231) This PR: - Updates reference to latest bioRxiv version. - Adds a reference to the Trajectory class to include it in doc compilation. --------- Co-authored-by: Ori Kronfeld --- docs/api/developer.md | 1 + docs/references.bib | 8 ++++---- docs/tutorials/index_scrna.md | 1 + docs/user_guide/index.md | 3 +++ docs/user_guide/models/decipher.md | 20 ++++++++++++++++++++ src/scvi/external/decipher/_model.py | 8 +++++--- 6 files changed, 34 insertions(+), 7 deletions(-) create mode 100644 docs/user_guide/models/decipher.md diff --git a/docs/api/developer.md b/docs/api/developer.md index fc435c31a3..fe9efc0366 100644 --- a/docs/api/developer.md +++ b/docs/api/developer.md @@ -283,4 +283,5 @@ Utility functions used by scvi-tools. utils.setup_anndata_dsp utils.attrdict model.get_max_epochs_heuristic + external.decipher.utils.Trajectory ``` diff --git a/docs/references.bib b/docs/references.bib index c6bff90f36..17e36ad060 100644 --- a/docs/references.bib +++ b/docs/references.bib @@ -222,12 +222,12 @@ @article{Martens2023 publisher={Nature Publishing Group} } -@article{Nazaret23, - title={Deep generative model deciphers derailed trajectories in acute myeloid leukemia}, - author={Nazaret, Achille and Fan, Joy Linyue and Lavallee, Vincent-Philippe and Cornish, Andrew E and Kiseliovas, Vaidotas and Masilionis, Ignas and Chun, Jaeyoung and Bowman, Robert L and Eisman, Shira E and Wang, James and others}, +@article{Nazaret24, + title={Joint representation and visualization of derailed cell states with Decipher}, + author={Nazaret, Achille and Fan, Joy Linyue and Lavall{\'e}e, Vincent-Philippe and Burdziak, Cassandra and Cornish, Andrew E and Kiseliovas, Vaidotas and Bowman, Robert L and Masilionis, Ignas and Chun, Jaeyoung and Eisman, Shira E and others}, journal={bioRxiv}, pages={2023--11}, - year={2023}, + year={2024}, publisher={Cold Spring Harbor Laboratory}, doi = {10.1101/2023.11.11.566719} } diff --git a/docs/tutorials/index_scrna.md b/docs/tutorials/index_scrna.md index 724a67f1ff..7d3603291b 100644 --- a/docs/tutorials/index_scrna.md +++ b/docs/tutorials/index_scrna.md @@ -18,5 +18,6 @@ notebooks/scrna/contrastiveVI_tutorial notebooks/scrna/scanvi_fix notebooks/scrna/MrVI_tutorial notebooks/scrna/sysVI +notebooks/scrna/decipher_tutorial notebooks/scrna/velovi ``` diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md index 49926ad2f0..06e18aabe7 100644 --- a/docs/user_guide/index.md +++ b/docs/user_guide/index.md @@ -48,6 +48,9 @@ scvi-tools is composed of models that can perform one or many analysis tasks. In * - :doc:`/user_guide/models/sysvi` - Integrating single-cell RNA-seq datasets with substantial batch effects - :cite:p:`Hrovatin23` + * - :doc:`/user_guide/models/decipher` + - Joint representation and visualization of derailed cell states with Decipher + - :cite:p:`Nazaret24` * - :doc:`/user_guide/models/velovi` - Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells - :cite:p:`GayosoWeiler23` diff --git a/docs/user_guide/models/decipher.md b/docs/user_guide/models/decipher.md new file mode 100644 index 0000000000..4e7d1f2164 --- /dev/null +++ b/docs/user_guide/models/decipher.md @@ -0,0 +1,20 @@ +# Decipher + +:::{note} +This page is under construction. +::: + +**decipher** (Python class {class}`~scvi.external.Decipher`) is a ... + +The advantages of Decipher are: + +- ... + +The limitations of Decipher include: + +- ... + +```{topic} Tutorials: + +- {doc}`/tutorials/notebooks/scrna/decipher_tutorial` +``` diff --git a/src/scvi/external/decipher/_model.py b/src/scvi/external/decipher/_model.py index 56a34bcfa5..a6b06e5f71 100644 --- a/src/scvi/external/decipher/_model.py +++ b/src/scvi/external/decipher/_model.py @@ -19,7 +19,7 @@ class Decipher(PyroSviTrainMixin, BaseModelClass): - """Decipher model for single-cell data analysis :cite:p:`Nazaret23`. + """Decipher model for single-cell data analysis :cite:p:`Nazaret24`. Parameters ---------- @@ -238,7 +238,8 @@ def compute_decipher_time( cluster_obs_key : str The key in adata.obs containing cluster assignments. trajectory : Trajectory - A Trajectory object containing the trajectory information. + A :class:`~scvi.external.decipher.utils.Trajectory` object containing + the trajectory information. n_neighbors : int The number of neighbors to use for the KNN regression. @@ -280,7 +281,8 @@ def compute_gene_patterns( adata : AnnData The annotated data matrix. trajectory : Trajectory - A Trajectory object containing the trajectory information. + A :class:`~scvi.external.decipher.utils.Trajectory` object containing + the trajectory information. l_scale : float The library size scaling factor. n_samples : int