def bc_chromosome_draw_label(self, cur_drawing, label_name):
"""Monkeypatch to Bio.Graphics.BasicChromosome.Chromosome._draw_label.
Draw a label for the chromosome. Mod: above the chromosome, not below.
"""
# Center on chromosome image
x_position = 0.5 * (self.start_x_position + self.end_x_position)
# Place at the bottom of the diagram?
y_position = self.start_y_position + 0.1 * inch # was: self.end_y_position
label_string = BC.String(x_position, y_position, label_name)
label_string.fontName = 'Times-BoldItalic'
label_string.fontSize = self.title_size
label_string.textAnchor = 'middle'
cur_drawing.add(label_string)
def bc_organism_draw(org, title, wrap=12):
"""Modified copy of Bio.Graphics.BasicChromosome.Organism.draw.
Instead of stacking chromosomes horizontally (along the x-axis), stack rows
vertically, then proceed with the chromosomes within each row.
Parameters
----------
org :
The chromosome diagram object being modified.
title : str
The output title of the produced document.
wrap : int
Maximum number of chromosomes per row; the remainder will be wrapped to
the next row(s).
"""
margin_top = 1.25 * inch
margin_bottom = 0.1 * inch
margin_side = 0.5 * inch
width, height = org.page_size
cur_drawing = BC.Drawing(width, height)
# Draw the title text
title_string = BC.String(width / 2, height - margin_top + .5 * inch, title)
title_string.fontName = 'Helvetica-Bold'
title_string.fontSize = org.title_size
title_string.textAnchor = "middle"
cur_drawing.add(title_string)
# Layout subcomponents (individual chromosomes), wrapping into rows
if len(org._sub_components) > 0:
nrows = math.ceil(len(org._sub_components) / wrap)
x_pos_change = (width - 2 * margin_side) / wrap
y_pos_change = (height - margin_top - margin_bottom) / nrows
cur_x_pos = margin_side
cur_row = 0
for i, sub_component in enumerate(org._sub_components):
if i % wrap == 0 and i != 0:
cur_row += 1
cur_x_pos = margin_side
# Set the page coordinates of the chromosome drawing
sub_component.start_x_position = cur_x_pos + 0.05 * x_pos_change
sub_component.end_x_position = cur_x_pos + 0.95 * x_pos_change
sub_component.start_y_position = (height - margin_top -
y_pos_change * cur_row)
sub_component.end_y_position = (margin_bottom + y_pos_change *
(nrows - cur_row - 1))
# Render the chromosome drawing
sub_component.draw(cur_drawing)
# Update the locations for the next chromosome
cur_x_pos += x_pos_change
# Draw a legend
# (Rect coordinates are: left, bottom, width, height)
# Bounding box -- near-bottom, center
cur_drawing.add(
BC.Rect(width / 2 - .8 * inch,
.5 * inch,
1.6 * inch,
.4 * inch,
fillColor=colors.white))
# Red box & label -- in left half of bounding box
cur_drawing.add(
BC.Rect(width / 2 - .7 * inch,
.6 * inch,
.2 * inch,
.2 * inch,
fillColor=colors.Color(.8, .2, .2)))
cur_drawing.add(
BC.String(width / 2 - .42 * inch,
.65 * inch,
"Gain",
fontName='Helvetica',
fontSize=12))
# Blue box & label -- in right half of bounding box
cur_drawing.add(
BC.Rect(width / 2 + .07 * inch,
.6 * inch,
.2 * inch,
.2 * inch,
fillColor=colors.Color(.2, .2, .8)))
cur_drawing.add(
BC.String(width / 2 + .35 * inch,
.65 * inch,
"Loss",
fontName='Helvetica',
fontSize=12))
# Let the caller take care of writing to the file...
return cur_drawing
