Library

Main function : ontosunburst

from ontosunburst import ontosunburst

Main function to be called generating the sunburst figure

Parameters

Parameter	Type	Default	Values	Description
interest_set	List[str]			Interest set of concepts to classify. List of the ontology ID's.
ontology	str	None	'metacyc' 'ec' 'chebi' 'chebi_r' 'kegg' 'go_cc' 'go_bp' 'go_mf' 'go' None	Ontology to use (or None if personal ontology)
abundances	List[str]	None		Abundance values associated to interest_set list parameter. (List of abundances : indexes matching corresponding interest_set ID's)
reference_set	List[str]	None		Reference set of concepts. List of the ontology ID's.
ref_abundances	List[str]	None		Abundance values associated to reference_set list parameter. (List of abundances : indexes matching corresponding reference_set ID's)
analysis	str	'topology'	'topology' 'enrichment'	Analysis mode : topology or enrichment.
output	str	'sunburst'		Path of the output to save figure. (Path + base output name) If None, outputs will be sunburst.html and sunburst.tsv files
scores	Dict[str, float]	None		Dictionary associating for each ontology ID, its enrichment score. If None enrichment will be calculated.
write_output	bool	True		True to write the html figure and tsv class files, False to only return plotly sunburst figure
ontology_dag_input	str Dict[str, str]	None		Ontology DAG dictionary or json file. Dictionary associating to each concept ID of the ontology, the list of their +1 parent concepts.
input_root	str	None		Root item of the ontology. (To precise only if tailored ontology)
id_to_label_input	str Dict[str, str]	None		ID to Label correspondance dictionary (associating ontology ID to a label) or path to corresponding json file If None will use default files.
labels	bool	True		True to use labels as labels, False to use IDs otherwise.
test	str	'binomial'	'binomial' 'hypergeometric'	Type of test if analysis=enrichment : binomial or hypergeometric test.
root_cut	str	'cut'	'uncut' 'cut' 'total'	Mode for root cutting (uncut, cut or total)
path_cut	str	'uncut'	'uncut' 'deeper' 'higher' 'bound'	Mode for nested path cutting (uncut, deeper, higher or bound)
ref_base	bool	False		True to have the base classes representation of the reference set in the figure.
show_leaves	bool	False		True to show input concepts at sunburst leaves
**kwargs				Additional arguments (figure options)

Additional arguments : Kwargs

Kwarg	Type	Default Topology	Default Enrichment	Values	Description
c_min	float	1	-10		Minimal value
c_max	float	None	10		Maximal value
c_mid	float	None	0		Mid value
max_depth	int	7	7	>1	Maximal sunburst depth
colorscale	str	Viridis	RdBu	plotly colorscale name	Colorscale
title	str	'{output} : Proportion of classes'	'{output} : Classes enrichment representation'		Title of figure
colorbar_legend	str	'Count'	'Log10(pvalue)'		Legend of colorbar
bg_color	str	'rgba(255, 255, 255, 0)'	'rgba(255, 255, 255, 0)'	name or hex or rgba	Figure background color
font_color	str	'#111111'	'#111111'	name or hex or rgba	Font color
font_size	int	20	20	>1	Font size
table_title	str		'Significant p-values'		Enrichment table title
table_legend	str		'IDs'		Enrichment table ID's name
table_color	str		'#666666'	name or hex or rgba	Enrichment table cases color

Returns

Type	Description
graph_objects.Figure	Plotly graph_objects figure of the sunburst

Examples

from ontosunburst import ontosunburst

INT_LST = ['CPD-24674', 'CPD-24687', 'CPD-24688']
REF_LST = ['CPD-24674', 'CPD-24687', 'CPD-24688',
           'CPD-12782', 'CPD-12784', 'CPD-12787',
           'CPD-12788', 'CPD-12789', 'CPD-12796',
           'CPD-12797', 'CPD-12798', 'CPD-12805',
           'CPD-12806', 'CPD-12812', 'CPD-12816',
           'CPD-1282', 'CPD-12824', 'CPD-1283']

fig = ontosunburst(interest_set=INT_LST, ontology='metacyc', abundances=None, 
                   reference_set=REF_LST, ref_abundances=None, analysis='topology', 
                   output='mc7', scores=None, write_output=False,
                   ontology_dag_input=None, input_root=None, id_to_label_input=True, 
                   labels=True, test='binomial', root_cut='cut', path_cut='uncut',
                   ref_base=True, show_leaves=True)

# EQUIVALENT TO :

fig = ontosunburst(interest_set=INT_LST, ontology='metacyc', reference_set=REF_LST, 
                   output='mc7', write_output=False, ref_base=True, show_leaves=True)