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carmonalab / ProjecTILs

Interpretation of cell states using reference single-cell maps
GNU General Public License v3.0
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How to use Run.Projectils with Harmony. #63

Closed mckoch234 closed 11 months ago

mckoch234 commented 11 months ago

I tried using reduction ="harmony" with run.projectils but it's giving me an error saying there are no cell embeddings, even though there are cell embeddings in the reduction.

mass-a commented 11 months ago

Hi, the reduction parameter refers to the low-dimensional space in which to calculate nearest neighbors between cells of the reference and projected cells of the query, and in this way assign predicted labels. The references do not have a "harmony" embedding (default is 'pca'). We can improve the documentation to avoid confusion.