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mavis.illustrate.diagram

This is the primary module responsible for generating svg visualizations

HEX_WHITE

HEX_WHITE = '#FFFFFF'

HEX_BLACK

HEX_BLACK = '#000000'

mavis.illustrate.diagram.draw_sv_summary_diagram()

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

def 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,
    stack_reference_transcripts=False,
):

Args

  • config
  • ann (Annotation): the annotation object to be illustrated
  • reference_genome (Dict[str,str]): reference sequences

  • templates (List[Template]): list of templates, used in drawing the template-level view

  • template_display_label_prefix (str): the character to precede the template label

  • draw_reference_transcripts
  • draw_reference_genes
  • draw_reference_templates
  • draw_fusion_transcript
  • stack_reference_transcripts