topiary.reports.cards

topiary.reports.cards.ancestor

Functions for generating bootstrap cards with various types of information on them.

topiary.reports.cards.ancestor.create_ancestor_card(anc_dict, output_directory, ancestor_directory, event_color, event_name)

Create a card holding all of the ancestors as individual accordion entries.

topiary.reports.cards.asr_tree

topiary.reports.cards.asr_tree.create_asr_tree_card(supervisor, output_directory, ancestor_directory, T)

topiary.reports.cards.duplications

Functions for checking the quality of an ancestral inference.

topiary.reports.cards.duplications.create_duplications_card(supervisor, T, p_column)

Create a card warning if there are more duplications than expected.

Parameters:

• supervisor (topiary.Supervisor instance) – supervisor with calculation loaded

• T (ete3.Tree) – tree with events loaded

• p_column (str) – column in supervisor.df that holds the paralogs calls

Returns:

html – html warning. If no warning is needed, returns and empty string.

Return type:

str

topiary.reports.cards.input

topiary.reports.cards.input.create_input_card(supervisor, p_column=None)

Create a card describing the input to the analysis.

topiary.reports.cards.model

topiary.reports.cards.model.create_model_card(supervisor, output_directory)

topiary.reports.cards.param

topiary.reports.cards.param.create_param_card(supervisor, anc_dict, ancestor_directory)

topiary.reports.cards.species_tree

topiary.reports.cards.species_tree.create_species_tree_card(supervisor, output_directory)