Add umap into cisTopic object?

[zhangqc723]

How to add a existing UMAP files into cisTopic object rather than runing run_umap？

[SeppeDeWinter]

Hi @zhangqc723

I migrated your question to the discussions tab.

You can add these as a pandas DataFrame to the projections attribute of the cistopic object.

For example,

import numpy as np
import pandas as pd
your_umap = pd.DataFrame(
    np.zeros((len(cistopic_obj.cell_names), 2)),
    columns = ["UMAP_1", "UMAP_2"], index = cistopic_obj.cell_names)
cistopic_obj.projections["cell"]["your_umap"] = your_umap #it's important to use the "cell" key here, cistopic object can also store dimensionality reductions for regions.

Best,

Seppe

[zhangqc723]

Thanks for you patient response

[SeppeDeWinter]

No worries!