Manu Setty comments

Results 36 comments of


                                            Manu Setty

cell-cell affinity matrix

We unfortunately do not have the functionality but it should be relatively straightforward to make this plot. The kernel matrix is stored in `model.K` and the order of cells is...

Many cells have zero non-trivial (>0.1) assignments

This is quite likely a result of specifying too many metacells. We do recommend the use of one metacell for 75-80 single-cells, but this is a function of the complexity...

Meaning and function of the `n_components` parameter

The `n_components` parameter is used below https://github.com/dpeerlab/Harmony/blob/eca0771348e7f1b901f95d1a8fc68d95530e830c/src/harmony/core.py#L48 to compute the principal components. In line 67, `temp` is already pre-computed principal components and thus the parameter is not passed for nearest...

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

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...

scikit-learn dependency

Thanks a lot for pointing this out Adam - we will have this fixed. Sorry for such a delayed response!

Request for barcode mapping in human_cd34_bm_rep1.h5ad

Hello - this is described here: https://github.com/dpeerlab/Palantir/issues/101

Manu Setty