early cell

[zhuzaicoder]

How to determine which cell to use for Palantir's early cell parameters?

[katosh]

Hi @zhuzaicoder, thanks for reaching out! Typically, the “early cell” is chosen based on your annotation. Because diffusion components often capture differentiation trajectories, we usually assume one of them reflects a “stemness” state within the set of cells labeled as early. To aid in this selection, we’ve introduced the palantir.utils.early_cell function, which finds a cell within the annotated group that sits at the extreme end of an early diffusion component. You can use it, e.g., with:

palantir.utils.early_cell(adata, early_celltype, celltype_column)