Comments (4)
I know how to fix the error 1:
chriscainx/mnnpy#30
I need to make the numba=0.45.0 and llvmlite 0.30.0, but it may be incompatible with others. So I give up mnn.
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I have updated the metrics.py from the scib in github. And the error 2 becomes:
Traceback (most recent call last):
File "scripts/metrics/metrics.py", line 263, in <module>
trajectory_=trajectory_
File "/data/msun/miniconda3/envs/scib-pipeline-R4.0/lib/python3.7/site-packages/scib/metrics/metrics.py", line 340, in metrics
verbose=False,
File "/data/msun/miniconda3/envs/scib-pipeline-R4.0/lib/python3.7/site-packages/scib/metrics/silhouette.py", line 113, in silhouette_batch
sil_df = pd.concat(sil_dfs).reset_index(drop=True)
File "/data/msun/miniconda3/envs/scib-pipeline-R4.0/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 295, in concat
sort=sort,
File "/data/msun/miniconda3/envs/scib-pipeline-R4.0/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 342, in __init__
raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
But I don't know how to fix it.
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Hi, it seems like you might not be getting any values for the batch silhouette (batch ASW) score. Could you check what the result of the metric is on the integrated output that is causing the error?
import scib
asw_batch = scib.me.silhouette_batch(
adata_int,
batch_key=batch_key,
group_key=label_key,
embed='X_emb',
return_all=True,
verbose=True,
)
If return_all
is True, you will get a Dataframe instead of an overall metric. I'm guessing it is empty in your case.
If 'X_emb' is not available, try computing and using the PCA instead
asw_batch = scib.me.silhouette_batch(
adata_int,
batch_key=batch_key,
group_key=label_key,
embed='X_pca',
return_all=True,
verbose=True,
)
from scib-pipeline.
I changed the code so that you get NaN if the dataframe is empty. Feel free to update scib and rerun the pipeline.
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