Closed lizgehret closed 1 year ago
Here is what the updated output & resultant viz looks like:
Okay I think this is ready for a final review @ebolyen - I'm going to open a separate PR for the usage example that includes back ticks in the formula once I have #100 sorted, but the rest of this should be all set.
Note: the dataloaf output's index has been changed from feature-id
to id
since we are discouraging the use of dashes in metadata columns when using ancombc (due to the issues mentioned above).
This PR fixes a couple of small bugs, and adds some additional testing.
The following bugs have been fixed:
A bug in the
tabulate
visualizer that would fail to create a visualization if 'id' was not present within the input table. This machinery worked with the ancombc R package version 3.15, but the output was modified slightly in 3.16 and instead of an 'id' column, there is now a 'taxon' column that represents the feature IDs. The index column has been re-named 'feature-id' and the index is pulled by column location instead of 'id' within the visualizer.A bug that unintentionally writes the
input.biom.tsv
andinput.map.txt
files (used for ancombc inputs) to the user's CWD. This was originally added for de-bugging purposes and was never removed.The following tests have been added:
A usage example for
qiime composition tabulate
A unit test for the FrictionlessCSV -> DataFrame transformer
Some additional misc. items within this PR include:
Updating naming conventions for usage examples, tests, and test data to specify the ancombc method (to prevent confusion between ancom and ancombc).
Updating the copyright year to 2023