Things with confusing names

[spficklin]

This issue is meant as a catch all for items that are confusing. I'll put things as checkboxes so as they get resolved they can be checked off. Once @biggstd is satisfied that all confusing named items are corrected this can get closed out.

• count_mask in the get_gem_data function is meant to indicate how to handle missing values in GEMs. I think it's trying to do too much in one argument. Perhaps it might be better as two argument.s First could be missing and the user specifies the numeric value to use for missing: 0 or NaN (defaults to 0). The second argument could be drop_missing which can be boolean and is meant to drop genes (columns I think) that have missing values.