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Scale #2457
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Scale #2457
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Codecov Report
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- Coverage 71.88% 71.76% -0.12%
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Lines 11510 11537 +27
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+ Hits 8274 8280 +6
- Misses 3236 3257 +21
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@Sakshi-2797 is there a reason why you'd introduce a flavor here instead of outright replacing the implementation? |
Hi @Zethson , |
Unfortunately, I run into
When trying to use the new flavor with the existing test. |
Hi @Zethson , |
Signed-off-by: zethson <[email protected]>
Please adapt the corresponding test to:
It fails for me with |
I pushed to your branch. It failed yesterday while Github was having issues. The test should pass. |
@Sakshi-2797 were you able to find the fix to make it work or do you need more information? I'm happy to take over your branch as soon as it works to glue things together |
Hi @Zethson , |
Sparse matrices are absolutely essential for single-cell to ensure that RAM usage is kept low. Is there a way to make your implementation work with sparse matrices? |
Sorry for the delay in responding here. Our resources got pulled into other projects. We are looking to make it work with sparse matrices. |
This contribution holds modifications to the existing 'scale function' which turns out to be a faster implementation than the original one. We have introduced flavors - default and use_fastpp , where use_fastpp is our faster implementation of the scale function.The scale function modification provides an overall speedup of approx ~2x in comparison to the already existing 'scale' function.
Usage : sc.pp.scale(adata,max_value=10,flavor='use_fastpp')