BUGFIX: changed raise ValueError in align_track_with_cooler to just a…

[kannandeepti]

proposed BUGFIX: changed raise ValueError in align_track_with_cooler to just a warning

Previously, the align_track_with_cooler() function raised a Value
Error if the track values of a given region in the viewframe were
all NaN. However, this check is not necessary because NaN values
are anyways already masked.

[agalitsyna]

Hey, @gfudenberg. Is there a reason why empty regions in align track with cooler give an error rather than a warning? (Authorship deduced from git blame)

I'm thinking about Deepti's case: why would one chromosome having all NaNs in the dataframe before assignment constitute an issue in the downstream analysis?

[gfudenberg]

Hi-- I don't know if I quite understand Deepti's case, but I think we discussed this in
#271
#180 (comment)
and the idea was that you should pass a view that does not have the offending chromosome, since it is one line. It may have helped streamline assumptions in some downstream applications as well (saddles?)

[agalitsyna]

Thanks for getting back to it! I think the non-trivial thing here is that align_track_with_cooler does not distinguish absent bins in the track and NaN values in the track, and it's not entirely clear why.
Imagine that some chromosome has all NaNs in the track (e.g. some mark is completely absent on this chromosome). It's expected that the bins from this chromosome do not contribute to aggregation, but why would this cause an error?

The solution might be to raise an error only if the chromosome is completely absent form the track (or some bins of it, as you propose in #271).

[gfudenberg]

Maybe it is the use in functions like cis_eig? E.g. if there is this all NaN chromosome, maybe this would throw an error when you try to correlate?

cooltools/cooltools/api/eigdecomp.py

Line 435 in 45a56df

phasing_track_region_values = phasing_track_region["value"].values

[agalitsyna]

Okay, these are all good points that we discuss here. I introduced the parameter for ignoring missing values in alignment, and add it as a control option for saddle (because the chromosomes with all NaNs do not really affect the output). For eigdecomp you are right, @gfudenberg , there should be at least some value per each chromosome, otherwise phasing does not make sense. I set this new parameter to default True in eigdecomp.

To sum up, this is small update of align_track_with_cooler, but might be important to those practicing various types of saddles.

[agalitsyna]

Illustration of the problem before and after the fix:

[gfudenberg]

maybe consider
drop_track_nas --> drop_track_na