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# Copyright 2001 by Brad Chapman. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Display information distributed across a Chromosome-like object.
These classes are meant to show the distribution of some kind of information
as it changes across any kind of segment. It was designed with chromosome
distributions in mind, but could also work for chromosome regions, BAC clones
or anything similar.
Reportlab is used for producing the graphical output.
"""
# standard library
import math
# reportlab
from reportlab.lib.pagesizes import letter
from reportlab.lib.units import inch
from reportlab.lib import colors
from reportlab.graphics.shapes import Drawing, String
from reportlab.graphics.charts.barcharts import VerticalBarChart
from reportlab.graphics.charts.barcharts import BarChartProperties
from reportlab.graphics.widgetbase import TypedPropertyCollection
from Bio.Graphics import _write
class DistributionPage:
"""Display a grouping of distributions on a page.
This organizes Distributions, and will display them nicely
on a single page.
"""
def __init__(self, output_format="pdf"):
"""Initialize the class."""
self.distributions = []
# customizable attributes
self.number_of_columns = 1
self.page_size = letter
self.title_size = 20
self.output_format = output_format
def draw(self, output_file, title):
"""Draw out the distribution information.
Arguments:
- output_file - The name of the file to output the information to,
or a handle to write to.
- title - A title to display on the graphic.
"""
width, height = self.page_size
cur_drawing = Drawing(width, height)
self._draw_title(cur_drawing, title, width, height)
# calculate the x and y position changes for each distribution
cur_x_pos = inch * 0.5
end_x_pos = width - inch * 0.5
cur_y_pos = height - 1.5 * inch
end_y_pos = 0.5 * inch
x_pos_change = (end_x_pos - cur_x_pos) / self.number_of_columns
num_y_rows = math.ceil(len(self.distributions) / self.number_of_columns)
y_pos_change = (cur_y_pos - end_y_pos) / num_y_rows
self._draw_distributions(
cur_drawing, cur_x_pos, x_pos_change, cur_y_pos, y_pos_change, num_y_rows
)
self._draw_legend(cur_drawing, 2.5 * inch, width)
return _write(cur_drawing, output_file, self.output_format)
def _draw_title(self, cur_drawing, title, width, height):
"""Add the title of the figure to the drawing (PRIVATE)."""
title_string = String(width / 2, height - inch, title)
title_string.fontName = "Helvetica-Bold"
title_string.fontSize = self.title_size
title_string.textAnchor = "middle"
cur_drawing.add(title_string)
def _draw_distributions(
self,
cur_drawing,
start_x_pos,
x_pos_change,
start_y_pos,
y_pos_change,
num_y_drawings,
):
"""Draw all of the distributions on the page (PRIVATE).
Arguments:
- cur_drawing - The drawing we are working with.
- start_x_pos - The x position on the page to start drawing at.
- x_pos_change - The change in x position between each figure.
- start_y_pos - The y position on the page to start drawing at.
- y_pos_change - The change in y position between each figure.
- num_y_drawings - The number of drawings we'll have in the y
(up/down) direction.
"""
for y_drawing in range(int(num_y_drawings)):
# if we are on the last y position, we may not be able
# to fill all of the x columns
if (y_drawing + 1) * self.number_of_columns > len(self.distributions):
num_x_drawings = (
len(self.distributions) - y_drawing * self.number_of_columns
)
else:
num_x_drawings = self.number_of_columns
for x_drawing in range(num_x_drawings):
dist_num = y_drawing * self.number_of_columns + x_drawing
cur_distribution = self.distributions[dist_num]
# find the x and y boundaries of the distribution
x_pos = start_x_pos + x_drawing * x_pos_change
end_x_pos = x_pos + x_pos_change
end_y_pos = start_y_pos - y_drawing * y_pos_change
y_pos = end_y_pos - y_pos_change
# draw the distribution
cur_distribution.draw(cur_drawing, x_pos, y_pos, end_x_pos, end_y_pos)
def _draw_legend(self, cur_drawing, start_y, width):
"""Add a legend to the figure (PRIVATE).
Subclasses can implement to provide a specialized legend.
"""
pass
class BarChartDistribution:
"""Display the distribution of values as a bunch of bars."""
def __init__(self, display_info=None):
"""Initialize a Bar Chart display of distribution info.
Attributes:
- display_info - the information to be displayed in the distribution.
This should be ordered as a list of lists, where each internal list
is a data set to display in the bar chart.
"""
if display_info is None:
display_info = []
self.display_info = display_info
self.x_axis_title = ""
self.y_axis_title = ""
self.chart_title = ""
self.chart_title_size = 10
self.padding_percent = 0.15
def draw(self, cur_drawing, start_x, start_y, end_x, end_y):
"""Draw a bar chart with the info in the specified range."""
bar_chart = VerticalBarChart()
if self.chart_title:
self._draw_title(
cur_drawing, self.chart_title, start_x, start_y, end_x, end_y
)
# set the position of the bar chart
x_start, x_end, y_start, y_end = self._determine_position(
start_x, start_y, end_x, end_y
)
bar_chart.x = x_start
bar_chart.y = y_start
bar_chart.width = abs(x_start - x_end)
bar_chart.height = abs(y_start - y_end)
# set the information in the bar chart
bar_chart.data = self.display_info
bar_chart.valueAxis.valueMin = min(self.display_info[0])
bar_chart.valueAxis.valueMax = max(self.display_info[0])
for data_set in self.display_info[1:]:
if min(data_set) < bar_chart.valueAxis.valueMin:
bar_chart.valueAxis.valueMin = min(data_set)
if max(data_set) > bar_chart.valueAxis.valueMax:
bar_chart.valueAxis.valueMax = max(data_set)
# set other formatting options
if len(self.display_info) == 1:
bar_chart.groupSpacing = 0
style = TypedPropertyCollection(BarChartProperties)
style.strokeWidth = 0
style.strokeColor = colors.green
style[0].fillColor = colors.green
bar_chart.bars = style
# set the labels
# XXX labels don't work yet
# bar_chart.valueAxis.title = self.x_axis_title
# bar_chart.categoryAxis.title = self.y_axis_title
cur_drawing.add(bar_chart)
def _draw_title(self, cur_drawing, title, start_x, start_y, end_x, end_y):
"""Add the title of the figure to the drawing (PRIVATE)."""
x_center = start_x + (end_x - start_x) / 2
y_pos = end_y + (self.padding_percent * (start_y - end_y)) / 2
title_string = String(x_center, y_pos, title)
title_string.fontName = "Helvetica-Bold"
title_string.fontSize = self.chart_title_size
title_string.textAnchor = "middle"
cur_drawing.add(title_string)
def _determine_position(self, start_x, start_y, end_x, end_y):
"""Calculate the position of the chart with blank space (PRIVATE).
This uses some padding around the chart, and takes into account
whether the chart has a title. It returns 4 values, which are,
in order, the x_start, x_end, y_start and y_end of the chart
itself.
"""
x_padding = self.padding_percent * (end_x - start_x)
y_padding = self.padding_percent * (start_y - end_y)
new_x_start = start_x + x_padding
new_x_end = end_x - x_padding
if self.chart_title:
new_y_start = start_y - y_padding - self.chart_title_size
else:
new_y_start = start_y - y_padding
new_y_end = end_y + y_padding
return new_x_start, new_x_end, new_y_start, new_y_end
class LineDistribution:
"""Display the distribution of values as connected lines.
This distribution displays the change in values across the object as
lines. This also allows multiple distributions to be displayed on a
single graph.
"""
def __init__(self):
"""Initialize the class."""
pass
def draw(self, cur_drawing, start_x, start_y, end_x, end_y):
"""Draw a line distribution into the current drawing."""
pass
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