"""
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