Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

When `filter_obs` removes taxa should it remove data for those taxa from other data sets? #143

zachary-foster opened this issue Mar 23, 2018 · 1 comment


Copy link

@zachary-foster zachary-foster commented Mar 23, 2018

Currently, running filter_obs(obj, "my_data_set", some_condition, drop_taxa = TRUE) will remove taxa that no occur in "my_data_set" from the taxmap object, but it does not remove data in other data sets associated with removed taxa, so those end up with invalid taxon IDs.

  1. Only remove taxa that no longer appear in ALL data sets. The user could then use filter_taxa to remove all taxa from all data sets that don't appear in one of the data sets.
  2. Remove taxa from ALL data sets that are removed when filtering a single data set.

Perhaps 1 could be the default behavior and 2 could be optional. Maybe drop_other_obs = TRUE.

Either way, filter_obs should not be allowed to return an invalid taxmap object like it can now.


This comment has been minimized.

Copy link
Collaborator Author

@zachary-foster zachary-foster commented Mar 29, 2018

Solved this by using filter_taxa in filter_obs. I dont think filter_obs cannot return invalid taxmap objects now

@zachary-foster zachary-foster mentioned this issue Apr 5, 2018
3 of 3 tasks complete
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
None yet
1 participant
You can’t perform that action at this time.