Hi,
I am trying to use Palantir for mass cytometry data. I started first to reproduce the example data that you provided, however, I faced this error message:
dm_res = palantir.utils.run_diffusion_maps(pca_projections, n_components=5)
KeyError Traceback (most recent call last)
in
1 # Run diffusion maps
----> 2 dm_res = palantir.utils.run_diffusion_maps(pca_projections, n_components=5 ,knn=30, n_jobs=-1, alpha=0)
~/.local/lib/python3.7/site-packages/palantir/utils.py in run_diffusion_maps(data_df, n_components, knn, n_jobs, alpha)
41 temp = sc.AnnData(data_df.values)
42 sc.pp.neighbors(temp, n_pcs=0, n_neighbors=knn)
---> 43 kNN = temp.uns['neighbors']['distances']
44
45 # Adaptive k
KeyError: 'distances'
could you please help me to figure out what is going wrong?
Thanks in advance,
Zeinab
awnimo
commented
4 years ago
Hi, I am trying to use Palantir for mass cytometry data. I started first to reproduce the example data that you provided, however, I faced this error message: dm_res = palantir.utils.run_diffusion_maps(pca_projections, n_components=5)
KeyError Traceback (most recent call last)