diagram module

This is the primary module responsible for generating svg visualizations

mavis.illustrate.diagram.draw_multi_transcript_overlay(config, gene, vmarkers=None, window_buffer=0, plots=None)

mavis.illustrate.diagram.draw_sv_summary_diagram(config, ann, reference_genome=None, templates=None, ignore_absent_templates=True, user_friendly_labels=True, template_display_label_prefix='', draw_reference_transcripts=True, draw_reference_genes=True, draw_reference_templates=True, draw_fusion_transcript=True)

this is the main drawing function. It decides between layouts where each view-level is split into one or two diagrams (side-by-side) dependant on whether the event is interchromosomal, within a single transcript, etc.

Diagrams have four levels

• template
• gene
• transcript
• fusion transcript/translation

Parameters:

• ann (Annotation) – the annotation object to be illustrated
• reference_genome (dict of str by str) – reference sequences
• templates (list of Template) – list of templates, used in drawing the template-level view
• ignore_absent_templates (bool) – if true then will not raise an error if the template information is not given but will not draw the template instead
• show_template (bool) – if false the template-level view is not drawn
• user_friendly_labels (bool) – if True, genes are labelled by their aliases (where possible) and domains are labeled by their names (where possible)
• template_display_label_prefix (str) – the character to precede the template label