RuntimeWarning: divide by zero encountered in true_divide dists = dists ** 2/(scaling_factors.values[rows] ** 2)

[fangfang0906]

Dear authors,

Thanks for developing harmony! It's really cool! I got this warning "RuntimeWarning: divide by zero encountered in true_divide " when following standard pipeline and the embedding looks a little weird.

Do you have any idea what's the possible reasons?

[ManuSetty]

Thank you for interest in Harmony. A could of questions:

1. Do you encounter this issue with the example dataset too?
2. Do you have any cells with 0 counts for all genes in our dataset?