milopy
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emdann
Python implementation of Milo for differential abundance testing on KNN graph
Hi Emma, Really looking forward to trying the Milo implementation in Python. When I run: `milo.make_nhoods(adata_LP_ILE, prop=0.1) ` I get the following error: ``` /home/jupyter/.local/lib/python3.7/site-packages/numpy/core/fromnumeric.py:3441: RuntimeWarning: Mean of empty slice....
The error: ```py milo.make_nhoods(adata, prop=0.05) ``` ```pytb InvalidIndexError: (array([ 6, 14, 31, 32, 36, 41, 44, 45, 46, 1226, 1893, 2742, 3122, 3475, 3494, 3578, 3588, 4416, 4446, 5146, 5274,...
Thank you for maintaining milopy! Regarding the function `plotNhoodExpressionDA` in https://github.com/MarioniLab/miloR/pull/31, is there a variant of this function exposed through this package? I think it is only R at the...
Hello, thank you for creating milopy! I have been using it quite often lately, but now I discovered an issue: When I start a Jupyterlab kernel, load milo as in...
Gathering some suggestions: - Patsy for model matrix encoding https://patsy.readthedocs.io/en/latest/overview.html - GLM implementation in `pymc3` https://docs.pymc.io/notebooks/GLM-poisson-regression.html
The original cell-level AnnData object and the sample x nhoods AnnData are stored in a common MuData object with `.mod` `cells` and `samples`. Samples are in `mdata["samples"].obs` and nhoods are...
Current implementation gives `KeyError` with missing `Nhood_size`
Thanks for the wonderful tool! I was wondering whether it would be okay to perform MILO analysis based on a different latent space and KNN than those used for building...
The problem seems to be at this step: dist_mat = knn_dists[nhood_ixs, :] whereby nhood_ixs is a 'Series'. It would work with: dist_mat = knn_dists[np.array(nhood_ixs), :] This seems to be a...
### Description When running `milo.count_nhoods` on my `adata` object, I encountered a `ValueError` indicating that the length of values does not match the length of the index. My code: ```python...
