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EBISPOT / scxa_2_cxg

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Extend CxG conversion to cover - `obsm` (embedding) #8

Closed dosumis closed 4 months ago

anitacaron commented 4 months ago

The obsm seems to have always the same embedding:

"X_pca",
"X_tsne_perplexity_1",
"X_tsne_perplexity_10",
"X_tsne_perplexity_15",
"X_tsne_perplexity_20",
"X_tsne_perplexity_25",
"X_tsne_perplexity_30",
"X_tsne_perplexity_35",
"X_tsne_perplexity_40",
"X_tsne_perplexity_45",
"X_tsne_perplexity_5",
"X_tsne_perplexity_50",
"X_umap_neighbors_n_neighbors_10",
"X_umap_neighbors_n_neighbors_100",
"X_umap_neighbors_n_neighbors_15",
"X_umap_neighbors_n_neighbors_20",
"X_umap_neighbors_n_neighbors_25",
"X_umap_neighbors_n_neighbors_3",
"X_umap_neighbors_n_neighbors_30",
"X_umap_neighbors_n_neighbors_5",
"X_umap_neighbors_n_neighbors_50"

Should we leave all the options or pick one of each?

anitacaron commented 4 months ago

Decided in the 2024-04-16 Meeting, all embedding will be available and use "X_umap_neighbors_n_neighbors_20" as default, to be added in uns.