def __process_loop_file(self):
interval_tree = {}
with opener(self.properties['file']) as f:
for idx, line in enumerate(f):
line = to_string(line)
# skip header line
if idx == 0 and self.__is_header(line):
continue
fields = line.split()
chr1, x1, x2, chr2, y1, y2, *other = fields
x1, x2, y1, y2 = list(map(int, [x1, x2, y1, y2]))
# skip inter-chromosome interaction
if chr1 != chr2:
continue
chromosome = chr1
if not chromosome.startswith("chr"):
chromosome = change_chrom_names(chromosome)
if chromosome not in interval_tree:
interval_tree[chromosome] = IntervalTree()
if len(other) == 0:
color = self.DEFAULT_COLOR
else:
rgb = other[0].split(",")
rgb = list(map(int, rgb))
color = rgb2hex(*rgb)
loop = self.LoopInverval(chr1, x1, x2, chr2, y1, y2, color)
interval_tree[chromosome].add(Interval(x1, y2, loop))
return interval_tree
def plot(self, ax, gr: GenomeRange, **kwargs):
regions = self.fetch_data(gr, **kwargs)
for (start, end, color) in regions:
if self.properties['color'] != 'bed_rgb':
color = self.properties['color']
if type(color) is not str:
color = rgb2hex(*color)
ax.axvspan(start, end, color=color, alpha=self.properties['alpha'])
if self.properties['border_line'] == 'yes':
# plot border line
ymin, ymax = ax.get_ylim()
ax.vlines([start, end], ymin, ymax,
linestyle=self.properties['border_line_style'],
linewidth=self.properties['border_line_width'],
color=self.properties['border_line_color'],
alpha=self.properties['border_line_alpha'])
def plot(self, ax, chrom_region, start_region, end_region):
regions = self.__get_regions(chrom_region, start_region, end_region)
for (start, end, color) in regions:
if self.properties['color'] != 'bed_rgb':
color = self.properties['color']
if type(color) is not str:
color = rgb2hex(*color)
ax.axvspan(start, end, color=color, alpha=self.properties['alpha'])
if self.properties['border_line'] == 'yes':
# plot border line
ymin, ymax = ax.get_ylim()
ax.vlines([start, end],
ymin,
ymax,
linestyle=self.properties['border_line_style'],
linewidth=self.properties['border_line_width'],
color=self.properties['border_line_color'],
alpha=self.properties['border_line_alpha'])