)
_beta_rarefaction_color_schemes = [
'BrBG', 'BrBG_r', 'PRGn', 'PRGn_r', 'PiYG', 'PiYG_r', 'PuOr', 'PuOr_r',
'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn',
'RdYlGn_r'
]
plugin.visualizers.register_function(
function=q2_diversity._beta.beta_rarefaction,
inputs={
'table': FeatureTable[Frequency],
'phylogeny': Phylogeny[Rooted]
},
parameters={
'metric': Str % Choices(beta.all_metrics()),
'clustering_method': Str % Choices({'nj', 'upgma'}),
'metadata': Metadata,
'sampling_depth': Int % Range(1, None),
# Need at least two iterations to do a comparison.
'iterations': Int % Range(2, None),
'correlation_method': Str % Choices({'spearman', 'pearson'}),
'color_scheme': Str % Choices(_beta_rarefaction_color_schemes)
},
input_descriptions={
'table':
'Feature table upon which to perform beta diversity '
'rarefaction analyses.',
'phylogeny':
'Phylogenetic tree containing tip identifiers that '
'correspond to the feature identifiers in the table. '
'samples may be grouped based on distinct values within a '
'metadata column.'),
)
_beta_rarefaction_color_schemes = [
'BrBG', 'BrBG_r', 'PRGn', 'PRGn_r', 'PiYG', 'PiYG_r',
'PuOr', 'PuOr_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r',
'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r']
plugin.visualizers.register_function(
function=q2_diversity._beta.beta_rarefaction,
inputs={
'table': FeatureTable[Frequency],
'phylogeny': Phylogeny[Rooted]},
parameters={
'metric': Str % Choices(beta.all_metrics()),
'clustering_method': Str % Choices({'nj', 'upgma'}),
'metadata': Metadata,
'sampling_depth': Int % Range(1, None),
# Need at least two iterations to do a comparison.
'iterations': Int % Range(2, None),
'correlation_method': Str % Choices({'spearman', 'pearson'}),
'color_scheme': Str % Choices(_beta_rarefaction_color_schemes)
},
input_descriptions={
'table': 'Feature table upon which to perform beta diversity '
'rarefaction analyses.',
'phylogeny': 'Phylogenetic tree containing tip identifiers that '
'correspond to the feature identifiers in the table. '
'This tree can contain tip ids that are not present in '
'the table, but all feature ids in the table must be '