diff --git a/docs/strategies/strategy_04.rst b/docs/strategies/strategy_04.rst new file mode 100644 index 0000000..6d0c6c2 --- /dev/null +++ b/docs/strategies/strategy_04.rst @@ -0,0 +1,37 @@ +Strategy 3: Manually refining UMAPs from selected embeddings (Napari GPU workaround) +======================================================== + +When to use it +-------------- + +Use this strategy as a workaround to refine UMAP embeddings if you don't use Napari on a machine with GPUs. + +What it does +------------ + +This strategy allows you to manually recalculate UMAP embeddings that you can then reload in the Napari GUI. + +How to use it +------------- + +1. Run the clustering workflow +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +This strategy works with the clustering workflow. Therefore run the clustering workflow including cluster selection in Napari, save the clusters that you would like to recalculate. + +2. Recalculate the UMAP from the embeddings from each cluster of interest. +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Now we manually recalculate the UMAP for each cluster we would like to refine. For example if you labeled your cluster cool_protein: + + .. prompt:: bash $ + + tomotwin_tools.py umap -i out/clustering/embeddings_cool_protein.temb -o out/clustering/refined/ + + +3. Visualize the refined UMAP in Napari +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Now you can load the refined UMAP in napari-boxmanager and look for subclusters that pick your protein of interest better + + diff --git a/docs/strategies/strategy_overview.rst b/docs/strategies/strategy_overview.rst index 46f7348..ecceff1 100644 --- a/docs/strategies/strategy_overview.rst +++ b/docs/strategies/strategy_overview.rst @@ -10,3 +10,6 @@ Strategies .. _strategy-03: .. include:: strategy_03.rst + +.. _strategy-04: +.. include:: strategy_04.rst \ No newline at end of file