Open mtvector opened 2 years ago
I figured out that if you set pynndescent_n_neighbors
to a lower number it solves this issue. Perhaps there should be an internal conditional or this!
Thanks for the kind words.
Good catch - I've already got a second condition in place for pynndescent, as it seems unable to process 10 or fewer observations no matter how you tweak the parameterisation:
In testing, it appears that the default pynndescent neighbour count of 30 runs just fine on data with 31 observations. You've got some super tiny batches going on, is that intentional?
Not intentional, but was working on a subsample of a huge dataset so it makes sense that a few of the batches ended up very small!
On Thu, Sep 30, 2021, 14:18 Krzysztof Polanski @.***> wrote:
Thanks for the kind words.
Good catch - I've already got a second condition in place for pynndescent, as it seems unable to process 10 or fewer observations no matter how you tweak the parameterisation:
In testing, it appears that the default pynndescent neighbour count of 30 runs just fine on data with 31 observations. You've got some super tiny batches going on, is that intentional?
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Reopening as I'll need to add a workaround into the code. This is not pressing as having 30 cell batches is not the most common.
Oops sorry!
Hi there, Having an issue when I try to run BBKNN without annoy. Had this error, then freshly installed everything in a new conda environment, I'm still getting the error passing from pynndescent when I run the code:
bbknn.bbknn(adata,batch_key='batch_name',use_annoy=False,metric='manhattan',neighbors_within_batch=3)
Thanks so much! This package works amazingly for correcting batch-driven compositional problems!!
Full error message below: