TypeError: Parameter 'metadata' received Metadata as an argument, which is incompatible with parameter type: MetadataColumn[Categorical]

[kristinachan]

TypeError: Parameter 'metadata' received Metadata as an argument, which is incompatible with parameter type: MetadataColumn[Categorical]

.get_column('name_of_column_w_categorical_type')

to check if column is numeric/categorical:

!metadata.actions.tabulate?
tabulate = metadata.actions.tabulate(sample_metadata)
tabulate.visualization #displays metadata table and whether columns numeric or categorical

e.g. .get_column('name_of_column_w_categorical_type')

uUniFrac_Subject_significance = diversity.actions.beta_group_significance(core_metrics.unweighted_unifrac_distance_matrix,
sample_metadata.get_column('name_of_column_w_categorical_type'))

[Oddant1 (Anthony Simard)]

Hello @kristinachan, what command did you run that created this error? It looks like you passed a Metadata object into a command that requires a Categorical column. In order to get a column you call .get_column("column name") on your Metadata object.

[kristinachan]

the original code that generated the error:

uUniFrac_Subject_significance = diversity.actions.beta_group_significance(core_metrics.unweighted_unifrac_distance_matrix,
sample_metadata)

^i.e. without .get_column()

Was trying to document how I solved it to improve documentation of errors. Thanks for the kind attention!

[Oddant1 (Anthony Simard)]

Oh, thank you! Has the issue been resolved?

[kristinachan]

Yes, thank you! much appreciated