# Copyright 2003-2008 by Leighton Pritchard. All rights reserved. # Revisions copyright 2008-2009 by Peter Cock. # # 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. # # Contact: Leighton Pritchard, The James Hutton Institute, # Invergowrie, Dundee, Scotland, DD2 5DA, UK # Leighton.Pritchard@hutton.ac.uk ################################################################################ """Graph module. Provides: - GraphData - Contains data from which a graph will be drawn, and information about its presentation For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com """ from math import sqrt from reportlab.lib import colors class GraphData: """Graph Data. Attributes: - id Unique identifier for the data - data Dictionary of describing the data, keyed by position - name String describing the data - style String ('bar', 'heat', 'line') describing how to draw the data - poscolor colors.Color for drawing high (some styles) or all values - negcolor colors.Color for drawing low values (some styles) - linewidth Int, thickness to draw the line in 'line' styles """ def __init__( self, id=None, data=None, name=None, style="bar", color=colors.lightgreen, altcolor=colors.darkseagreen, center=None, colour=None, altcolour=None, ): """Initialize. Arguments: - id Unique ID for the graph - data List of (position, value) tuples - name String describing the graph - style String describing the presentation style ('bar', 'line', 'heat') - color colors.Color describing the color to draw all or the 'high' (some styles) values (overridden by backwards compatible argument with UK spelling, colour). - altcolor colors.Color describing the color to draw the 'low' values (some styles only) (overridden by backwards compatible argument with UK spelling, colour). - center Value at which x-axis crosses y-axis. """ # Let the UK spelling (colour) override the USA spelling (color) if colour is not None: color = colour if altcolour is not None: altcolor = altcolour self.id = id # Unique identifier for the graph self.data = {} # holds values, keyed by sequence position if data is not None: self.set_data(data) self.name = name # Descriptive string # Attributes describing how the graph will be drawn self.style = style # One of 'bar', 'heat' or 'line' self.poscolor = color # Color to draw all, or 'high' values self.negcolor = altcolor # Color to draw 'low' values self.linewidth = 2 # linewidth to use in line graphs self.center = center # value at which x-axis crosses y-axis def set_data(self, data): """Add data as a list of (position, value) tuples.""" for pos, val in data: # Fill data dictionary self.data[pos] = val def get_data(self): """Return data as a list of sorted (position, value) tuples.""" data = [] for xval in self.data: yval = self.data[xval] data.append((xval, yval)) data.sort() return data def add_point(self, point): """Add a single point to the set of data as a (position, value) tuple.""" pos, val = point self.data[pos] = val def quartiles(self): """Return (minimum, lowerQ, medianQ, upperQ, maximum) values as tuple.""" data = sorted(self.data.values()) datalen = len(data) return ( data[0], data[datalen // 4], data[datalen // 2], data[3 * datalen // 4], data[-1], ) def range(self): """Return range of data as (start, end) tuple. Returns the range of the data, i.e. its start and end points on the genome as a (start, end) tuple. """ positions = sorted(self.data) # i.e. dict keys # Return first and last positions in graph # print(len(self.data)) return (positions[0], positions[-1]) def mean(self): """Return the mean value for the data points (float).""" data = list(self.data.values()) return sum(data) / len(data) def stdev(self): """Return the sample standard deviation for the data (float).""" data = list(self.data.values()) m = self.mean() runtotal = 0.0 for entry in data: runtotal += (entry - m) ** 2 # This is sample standard deviation; population stdev would involve # division by len(data), rather than len(data)-1 return sqrt(runtotal / (len(data) - 1)) def __len__(self): """Return the number of points in the data set.""" return len(self.data) def __getitem__(self, index): """Return data value(s) at the given position. Given an integer representing position on the sequence returns a float - the data value at the passed position. If a slice, returns graph data from the region as a list or (position, value) tuples. Slices with step are not supported. """ if isinstance(index, int): return self.data[index] elif isinstance(index, slice): # TODO - Why does it treat the end points both as inclusive? # This doesn't match Python norms does it? low = index.start high = index.stop if index.step is not None and index.step != 1: raise ValueError outlist = [] for pos in sorted(self.data): if pos >= low and pos <= high: outlist.append((pos, self.data[pos])) return outlist else: raise TypeError("Need an integer or a slice") def __str__(self): """Return a string describing the graph data.""" outstr = [f"\nGraphData: {self.name}, ID: {self.id}"] outstr.append("Number of points: %d" % len(self.data)) outstr.append(f"Mean data value: {self.mean()}") outstr.append(f"Sample SD: {self.stdev():.3f}") outstr.append( "Minimum: %s\n1Q: %s\n2Q: %s\n3Q: %s\nMaximum: %s" % self.quartiles() ) outstr.append("Sequence Range: %s..%s" % self.range()) return "\n".join(outstr)