obs and obsm in input h5ad Data

[ibimanji]

I found that your input h5ad data has coordinates in both obs and obsm. Are they both necessary? What is the difference between the x, y coordinates in obs and obsm? I think the cell location is described in obs, so what does the location in obsm mean?

[longyahui]

Hi,

Thanks for your questions.

The coordinates in obs and obsm are the same and are necessary, as our model is a graph-based method that considers adjacent relationships between cells to learn cell embeddings. Putting coordinates in obsm is to make graph construction and visualization more convenient. Hope it helps.

Best regards,
Yahui

[ibimanji]

Thank you very much for your response. What I am very confused about is that the input obs and obsm information are not the same. For example, in the tutorial2 you provided, I printed the obs and obsm for both modalities of the Dataset3_Mouse_thymus1 dataset as follows. They don’t appear to be the same. Could you please explain what kind of processing was done?