Reconstruction with Marker Warning

[Hofphi]

Hello everyone,

first of all I must say that I am very grateful for this awesome package!

Recently, I was running into a non-descriptive warning message when executing my script to do tissue reconstruction with marker genes. The script finishes and produces my desired output which looks like I expected.

However, I wanted to report this warning since I am not sure what it means and if it somehow influences my results.

The following reconstruction step produces the warning message:

tissue_with_markers.reconstruct(alpha_linear=0.5)

Warning message that points to a site-package:

Reconstructing spatial information with 3 markers: 828 cells and 500 locations ... 
~/miniconda3/lib/python3.6/site-packages/ot/bregman.py:363: RuntimeWarning: overflow encountered in true_divide
v = np.divide(b, KtransposeU)

Warning: numerical errors at iteration 9
It.  |Err         
-------------------
    0|8.868000e-03|
Warning: numerical errors at iteration 18
Warning: numerical errors at iteration 21
Warning: numerical errors at iteration 18
Warning: numerical errors at iteration 16
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[MalteMederacke]

I guess, you try to devide something with 0? How does DGE matrix look like

[nukappa]

Hi @Hofphi thank you for the kind words and reporting the warning. We sometimes get these warnings due to sparse DGEs as @MalteMederacke mentioned. A quick remedy is to try with larger values of the epsilon parameter: 10e-3 or 10e-2 and so on, though this might find a suboptimal spatial reconstruction.