# 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. """ 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.""" def draw(self, cur_drawing, start_x, start_y, end_x, end_y): """Draw a line distribution into the current drawing."""