Problem of LAP

[mhtksc]

Hi, I try to run the LAP's tutorial, and I get a different result of kinetic_heatmap( HSC->Bas) as the fig1. GATA2 was expressed from high to low in my result, but your tutorial is the opposite. I don't known why it happened. And I don't know how this is sorted. Is it sorted from highest to lowest expressed value from HSC to Bas, or is it sorted by the importance of the developmental events? Thanks.

[Xiaojieqiu]

thanks for using dynamo! the y-axis is sorted by the predict time along the LAP path.

The gene itself (on x-axis) is sorted via the timing of the expression peak along the LAP path.

@dummyindex could you please take a close look at this to ensure the reproducibility?

[dummyindex]

Hi @mhtksc , Thanks for trying the LAP tutorial. I confirmed that in our notebook case, GATA2 is indeed from low to high, which is different from yours. Can you provide your notebook? We can take a look and see what makes the results different. From our new notebook set: https://dynamo-release.readthedocs.io/en/latest/notebooks/tutorial_hsc_dynamo_basophil_lineage/tutorial_hsc_dynamo_basophil_lineage.html

looks like GATA2 should go from low to high (expression) along the path from HSC->Bas, and GATA2's peak should appear later.

[mhtksc]

Hi @dummyindex I followed the tutorial step by step. The code is in the lap.zip. I can't download the data via dyn.sample_data.hematopoiesis(). I downloaded the data in https://pitt.box.com/shared/static/kyh3s4wrxdywupn9wk9r2j27vzlvk8vf.h5ad (hematopoiesis_v1.h5ad) from dynamo/sample_data.py lap.zip

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