Problem on running FastHigashi on Ramani et al. dataset about higashi

[ruochiz]

Hi,

The NaN loss is "expected", that's just an intermediate information and doesn't represent that it's actually NaN. I think the problem might occur from the "reordering" of the cells. (I mean you can see that there are three clusters in the UMAP, they just not correspond to the cell types) In Fast-Higashi, cells with better qualities are ordered automatically in front of the cells with bad qualities.

To fix that, load the "reorder.npy" under the input2cache_dir, and use that to reorder the label info by label = label[reorder].

Or... use the label_info loaded in the model instead (mode.label_info['cell type'] for instance.)

See details in the final visualization part here: https://github.com/ma-compbio/Fast-Higashi/blob/main/PFC%20tutorial.ipynb

That being said, I recognize how this can be confusing, and will release a fix to this problem such that the order is corrected automatically by parsing an option to the fetch_cell_embedding() function