| |
| |
| |
| |
| |
| |
| """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. |
| """ |
|
|
| import math |
|
|
| from reportlab.graphics.charts.barcharts import BarChartProperties |
| from reportlab.graphics.charts.barcharts import VerticalBarChart |
| from reportlab.graphics.shapes import Drawing |
| from reportlab.graphics.shapes import String |
| from reportlab.graphics.widgetbase import TypedPropertyCollection |
| from reportlab.lib import colors |
| from reportlab.lib.pagesizes import letter |
| from reportlab.lib.units import inch |
|
|
| 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 = [] |
|
|
| |
| 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) |
|
|
| |
| 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 (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] |
|
|
| |
| 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 |
|
|
| |
| 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 |
| ) |
| |
| 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) |
|
|
| |
| 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) |
|
|
| |
| 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 |
|
|
| |
| |
| |
| |
|
|
| 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.""" |
|
|
