Source code for mavis.illustrate.diagram

"""
This is the primary module responsible for generating svg visualizations

"""
from ..annotate.genomic import IntergenicRegion
from ..annotate.variant import FusionTranscript
from ..constants import STRAND, ORIENT, CODON_SIZE, GIESMA_STAIN
from ..error import DrawingFitError, NotSpecifiedError
from ..interval import Interval
from .elements import *
from .scatter import ScatterPlot, draw_scatter
from .util import *
from colour import Color
from svgwrite import Drawing
import re
import svgwrite

# draw gene level view
# draw gene box
HEX_WHITE = '#FFFFFF'
HEX_BLACK = '#000000'


[docs]def draw_sv_summary_diagram( DS, ann, fusion_transcript=None, reference_genome=None, templates=None, ignore_absent_templates=True, show_template=True, user_friendly_labels=True, template_display_label_prefix='c' ): """ 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 Args: ann (Annotation): the annotation object to be illustrated fusion_transcript (FusionTranscript): the fusion transcript built from this annotation 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 """ templates = dict() if templates is None else templates canvas = Drawing(size=(DS.width, 1000)) # just set the height for now and change later labels = LabelMapping() # keep labels consistent within the drawing y = DS.top_margin x = DS.left_margin dx_label_shift = DS.label_left_margin x += dx_label_shift drawing_width = DS.width - dx_label_shift - DS.left_margin - DS.right_margin # calculate the half-width for transcripts and genes etc half_drawing_width = (drawing_width - DS.inner_margin - dx_label_shift) / 2 second_drawing_shift = x + half_drawing_width + DS.inner_margin + dx_label_shift if show_template: try: template1 = templates[ann.transcript1.get_chr()] template2 = templates[ann.transcript2.get_chr()] if user_friendly_labels and template1.name: labels.set_key(template_display_label_prefix + template1.name, template1) if user_friendly_labels and template2.name: labels.set_key(template_display_label_prefix + template2.name, template2) h = [0] if template1 == template2: # single template g = draw_template( DS, canvas, template1, drawing_width, breakpoints=[ann.break1, ann.break2], labels=labels) canvas.add(g) g.translate(x, y) h.append(g.height) else: # multiple templates g = draw_template(DS, canvas, template1, half_drawing_width, breakpoints=[ann.break1], labels=labels) canvas.add(g) g.translate(x, y) h.append(g.height) g = draw_template(DS, canvas, template2, half_drawing_width, breakpoints=[ann.break2], labels=labels) canvas.add(g) g.translate(second_drawing_shift, y) h.append(g.height) y += max(h) except KeyError as err: if not ignore_absent_templates: raise err colors = dict() genes = set() genes1 = set() genes2 = set() legend = dict() for g in ann.genes_overlapping_break1: genes1.add(g) colors[g] = DS.gene1_color for g, d in ann.genes_proximal_to_break1: genes1.add(g) colors[g] = DS.gene1_color for g in ann.genes_overlapping_break2: genes2.add(g) colors.setdefault(g, DS.gene2_color) for g, d in ann.genes_proximal_to_break2: genes2.add(g) colors.setdefault(g, DS.gene2_color) if ann.transcript1: try: genes1.add(ann.transcript1.gene) colors[ann.transcript1.gene] = DS.gene1_color_selected for e in ann.transcript1.exons: colors[e] = DS.exon1_color except AttributeError: genes1.add(ann.transcript1) colors[ann.transcript1] = DS.gene1_color_selected if ann.transcript2: try: genes2.add(ann.transcript2.gene) colors.setdefault(ann.transcript2.gene, DS.gene2_color_selected) for e in ann.transcript2.exons: colors.setdefault(e, DS.exon2_color) except AttributeError: genes2.add(ann.transcript2) colors[ann.transcript2] = DS.gene2_color_selected # set all the labels so that they are re-used correctly aliases = {} alias_failure = False for gene in sorted(genes1 | genes2, key=lambda x: (str(x.get_chr()), x.start)): if alias_failure: break try: for alias in gene.aliases: if alias in aliases and aliases[alias] != gene: alias_failure = True break if len(gene.aliases) == 1: aliases[gene.aliases[0]] = gene else: for alias in gene.aliases: # can't label when multiple aliases[alias] = None except AttributeError: pass alias_by_gene = {} for k, v in aliases.items(): alias_by_gene[v] = k for gene in sorted(genes1 | genes2, key=lambda x: (str(x.get_chr()), x.start)): if isinstance(gene, IntergenicRegion): l = labels.add(gene, DS.region_label_prefix) elif user_friendly_labels and not alias_failure and gene in alias_by_gene: labels[alias_by_gene[gene]] = gene else: l = labels.add(gene, DS.gene_label_prefix) gheights = [0] if ann.interchromosomal: g = draw_genes(DS, canvas, genes1, half_drawing_width, [ann.break1], colors=colors, labels=labels) g.translate(x, y) canvas.add(g) gheights.append(g.height) # second gene view g = draw_genes(DS, canvas, genes2, half_drawing_width, [ann.break2], colors=colors, labels=labels) g.translate(second_drawing_shift, y) canvas.add(g) gheights.append(g.height) else: g = draw_genes(DS, canvas, genes1 | genes2, drawing_width, [ann.break1, ann.break2], colors=colors, labels=labels) g.translate(x, y) canvas.add(g) gheights.append(g.height) y += max(gheights) + DS.inner_margin theights = [0] # now the transcript level drawings if ann.transcript1 == ann.transcript2: try: g = canvas.g(class_='transcript') g = draw_ustranscript(DS, canvas, ann.transcript1, drawing_width, breakpoints=[ann.break1, ann.break2], labels=labels, colors=colors, reference_genome=reference_genome ) theights.append(g.height) g.translate(x, y) canvas.add(g) except AttributeError: pass # Intergenic region or None else: # separate drawings try: g = canvas.g(class_='transcript') g = draw_ustranscript(DS, canvas, ann.transcript1, half_drawing_width, breakpoints=[ann.break1], labels=labels, colors=colors, reference_genome=reference_genome ) theights.append(g.height) g.translate(x, y) canvas.add(g) except AttributeError: pass # Intergenic region or None try: g = canvas.g(class_='transcript') g = draw_ustranscript(DS, canvas, ann.transcript2, half_drawing_width, breakpoints=[ann.break2], labels=labels, colors=colors, reference_genome=reference_genome ) theights.append(g.height) g.translate(second_drawing_shift, y) canvas.add(g) except AttributeError: pass # Intergenic region or None y += max(theights) if max(theights) == 0: y -= DS.inner_margin # finally the fusion transcript level drawing if fusion_transcript: y += DS.inner_margin for exon in fusion_transcript.exons: old_ex = fusion_transcript.exon_mapping[exon.position] if old_ex in colors: colors[exon] = colors[old_ex] g = canvas.g(class_='transcript') g = draw_ustranscript(DS, canvas, fusion_transcript, drawing_width, colors=colors, labels=labels, reference_genome=reference_genome ) g.translate(x, y) canvas.add(g) y += g.height y += DS.bottom_margin canvas.attribs['height'] = y for label, obj in labels.items(): if label in legend: continue try: legend[label] = obj.to_dict() except AttributeError: legend[label] = str(obj) # now make the json legend return canvas, legend
[docs]def draw_multi_transcript_overlay(DS, gene, vmarkers=None, window_buffer=0, plots=None): vmarkers = [] if vmarkers is None else vmarkers plots = [] if plots is None else plots canvas = Drawing(size=(DS.width, 1000)) # just set the height for now and change later w = DS.width - DS.left_margin - DS.right_margin - DS.overlay_left_label - DS.padding labels = LabelMapping() # keep labels consistent within the drawing all_exons = set() colors = dict() for tx in gene.transcripts: for ex in tx.exons: all_exons.add(ex) colors[ex] = DS.exon1_color if tx.is_best_transcript else DS.exon2_color for tr in tx.transcripts: for tl in tr.translations: for dom in tl.domains: labels.set_key(dom.name, dom.name) st = min([max([gene.start - window_buffer, 1])] + [m.start for m in vmarkers] + [p.xmin for p in plots]) end = max([gene.end + window_buffer] + [m.end for m in vmarkers] + [p.xmax for p in plots]) mapping = generate_interval_mapping( all_exons, w, DS.exon_intron_ratio, DS.exon_min_width, min_inter_width=DS.min_width, start=st, end=end ) main_group = canvas.g(class_='overlay') x = DS.overlay_left_label + DS.padding y = DS.marker_top_margin for plot in plots: plot_group = draw_scatter(DS, canvas, plot, mapping) main_group.add(plot_group) plot_group.translate(x, y) y += plot.height + DS.padding * 2 regular_transcripts = sorted([tx for tx in gene.transcripts if not tx.is_best_transcript], key=lambda x: x.name) for tx in regular_transcripts: g = draw_exon_track(DS, canvas, tx, mapping, colors=colors) main_group.add(g) g.translate(x, y) t = canvas.text( tx.name, insert=( x - DS.padding, y + DS.track_height / 2 + DS.font_central_shift_ratio * DS.label_font_size ), fill=DS.label_color, style=DS.font_style.format(font_size=DS.label_font_size, text_anchor='end'), class_='label' ) main_group.add(t) y += DS.padding + DS.track_height best_transcripts = sorted([tx for tx in gene.transcripts if tx.is_best_transcript], key=lambda x: x.name) for tx in best_transcripts: for txx in tx.transcripts: labels[tx.name] = txx g = draw_ustranscript(DS, canvas, tx, mapping=mapping, colors=colors, labels=labels) main_group.add(g) g.translate(x, y) y += DS.padding + g.height y += DS.marker_bottom_margin # now draw the breakpoints overtop for i, m in enumerate(sorted(vmarkers)): s = Interval.convert_ratioed_pos(mapping, m.start) t = Interval.convert_ratioed_pos(mapping, m.end) px_itvl = Interval(s.start, t.end) bg = draw_vmarker(DS, canvas, m, px_itvl.length(), y, label=labels.add(m, DS.marker_label_prefix)) bg.translate(x + px_itvl.start, 0) main_group.add(bg) main_group.translate(DS.left_margin, DS.top_margin) y += DS.bottom_margin canvas.add(main_group) canvas.attribs['height'] = y return canvas