Problem in PerformanceWarning

Help scanpy
1

I have tried to get DEG in my different groups of cell clusters but there comes with ana warning:

PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`

It seemed that the problem occurs due to code in scanpy/tools/_rank_genes_groups.py line 394 396 399 409 420. Is there any idea on why it occurs and how to improve dealing with fragmented dataframe?

2

any updates on this? I’ve also bumped into the same issue while running rank_genes_groups on a relatively large dataset (~200k cells) and it crashes the operation. Scanpy 1.9.3 anndata 0.9.1