mavis/illustrate/diagram
This is the primary module responsible for generating svg visualizations
HEX_WHITE
HEX_WHITE = '#FFFFFF'
HEX_BLACK
HEX_BLACK = '#000000'
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: DiagramSettings,
ann: Annotation,
reference_genome: ReferenceGenome = None,
templates: List[Template] = None,
ignore_absent_templates: bool = True,
user_friendly_labels: bool = True,
template_display_label_prefix: str = '',
draw_reference_transcripts: bool = True,
draw_reference_genes: bool = True,
draw_reference_templates: bool = True,
draw_fusion_transcript: bool = True,
stack_reference_transcripts: bool = False,
):
Args
- config (DiagramSettings)
- ann (Annotation): the annotation object to be illustrated
- reference_genome (ReferenceGenome): 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 (
bool
) - draw_reference_genes (
bool
) - draw_reference_templates (
bool
) - draw_fusion_transcript (
bool
) - stack_reference_transcripts (
bool
)