elements module¶
This is the primary module responsible for generating svg visualizations
-
mavis.illustrate.elements.
draw_breakpoint
(DS, canvas, breakpoint, width, height, label='')[source]¶ Parameters: - canvas (svgwrite.drawing.Drawing) – the main svgwrite object used to create new svg elements
- breakpoint (Breakpoint) – the breakpoint to draw
- width (int) – the pixel width
- height (int) – the pixel height
Returns: the group element for the diagram
Return type:
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mavis.illustrate.elements.
draw_exon
(DS, canvas, exon, width, height, fill, label='', translation=None)[source]¶ generates the svg object representing an exon
Parameters: - canvas (svgwrite.drawing.Drawing) – the main svgwrite object used to create new svg elements
- exon (Exon) – the exon to draw
- width (int) – the pixel width
- height (int) – the pixel height
- fill (str) – the fill color to use for the exon
Returns: the group element for the diagram
Return type: Todo
add markers for exons with abrogated splice sites
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mavis.illustrate.elements.
draw_exon_track
(DS, canvas, transcript, mapping, colors=None, x_start=None, x_end=None, translation=None)[source]¶
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mavis.illustrate.elements.
draw_gene
(DS, canvas, gene, width, height, fill, label='', reference_genome=None)[source]¶ generates the svg object representing a gene
Parameters: - canvas (svgwrite.drawing.Drawing) – the main svgwrite object used to create new svg elements
- gene (Gene) – the gene to draw
- width (int) – the pixel width
- height (int) – the pixel height
- fill (str) – the fill color to use for the gene
Returns: the group element for the diagram
Return type:
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mavis.illustrate.elements.
draw_genes
(DS, canvas, genes, target_width, breakpoints=None, colors=None, labels=None, plots=None, masks=None)[source]¶ draws the genes given in order of their start position trying to minimize the number of tracks required to avoid overlap
Parameters: - canvas (svgwrite.drawing.Drawing) – the main svgwrite object used to create new svg elements
- target_width (int) – the target width of the diagram
- genes (
list
ofGene
) – the list of genes to draw - breakpoints (
list
ofBreakpoint
) – the breakpoints to overlay - colors (
dict
ofGene
andstr
) – dictionary of the colors assigned to each Gene as fill
Returns: - the group element for the diagram.
Has the added parameters of labels, height, and mapping
Return type:
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mavis.illustrate.elements.
draw_template
(DS, canvas, template, target_width, labels=None, colors=None, breakpoints=None)[source]¶
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mavis.illustrate.elements.
draw_transcript_with_translation
(DS, canvas, translation, labels, colors, mapping, reference_genome=None, x_start=None, x_end=None)[source]¶
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mavis.illustrate.elements.
draw_ustranscript
(DS, canvas, ust, target_width=None, breakpoints=[], labels=<mavis.illustrate.util.LabelMapping object>, colors={}, mapping=None, reference_genome=None, masks=None)[source]¶ builds an svg group representing the transcript. Exons are drawn in a track with the splicing information and domains are drawn in separate tracks below
if there are multiple splicing variants then multiple exon tracks are drawn
Parameters: - canvas (svgwrite.drawing.Drawing) – the main svgwrite object used to create new svg elements
- target_width (int) – the target width of the diagram
- t (Transcript) – the transcript being drawn
- exon_color (str) – the color being used for the fill of the exons
- utr_color (str) – the color for the fill of the UTR regions
- abrogated_splice_sites (
list
ofint
) – list of positions to ignore as splice sites - breakpoints (
list
ofBreakpoint
) – the breakpoints to overlay
Returns: - the group element for the transcript diagram
Has the added parameters of labels, height, and mapping
Return type:
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mavis.illustrate.elements.
draw_vmarker
(DS, canvas, marker, width, height, label='', color=None)[source]¶ Parameters: - canvas (svgwrite.drawing.Drawing) – the main svgwrite object used to create new svg elements
- breakpoint (Breakpoint) – the breakpoint to draw
- width (int) – the pixel width
- height (int) – the pixel height
Returns: the group element for the diagram
Return type: