# 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 ################################################################################ """Linear Drawer module. Provides: - LinearDrawer - Drawing object for linear diagrams For drawing capabilities, this module uses reportlab to draw and write the diagram: http://www.reportlab.com """ # ReportLab imports from reportlab.graphics.shapes import Drawing, Line, String, Group, Polygon from reportlab.lib import colors # GenomeDiagram imports from ._AbstractDrawer import AbstractDrawer, draw_box, draw_arrow from ._AbstractDrawer import draw_cut_corner_box, _stroke_and_fill_colors from ._AbstractDrawer import intermediate_points, angle2trig, deduplicate from ._FeatureSet import FeatureSet from ._GraphSet import GraphSet from math import ceil class LinearDrawer(AbstractDrawer): """Linear Drawer. Inherits from: - AbstractDrawer Attributes: - tracklines Boolean for whether to draw lines delineating tracks - pagesize Tuple describing the size of the page in pixels - x0 Float X co-ord for leftmost point of drawable area - xlim Float X co-ord for rightmost point of drawable area - y0 Float Y co-ord for lowest point of drawable area - ylim Float Y co-ord for topmost point of drawable area - pagewidth Float pixel width of drawable area - pageheight Float pixel height of drawable area - xcenter Float X co-ord of center of drawable area - ycenter Float Y co-ord of center of drawable area - start Int, base to start drawing from - end Int, base to stop drawing at - length Int, size of sequence to be drawn - fragments Int, number of fragments into which to divide the drawn sequence - fragment_size Float (0->1) the proportion of the fragment height to draw in - track_size Float (0->1) the proportion of the track height to draw in - drawing Drawing canvas - drawn_tracks List of ints denoting which tracks are to be drawn - current_track_level Int denoting which track is currently being drawn - fragment_height Float total fragment height in pixels - fragment_bases Int total fragment length in bases - fragment_lines Dictionary of top and bottom y-coords of fragment, keyed by fragment number - fragment_limits Dictionary of start and end bases of each fragment, keyed by fragment number - track_offsets Dictionary of number of pixels that each track top, center and bottom is offset from the base of a fragment, keyed by track - cross_track_links List of tuples each with four entries (track A, feature A, track B, feature B) to be linked. """ def __init__( self, parent=None, pagesize="A3", orientation="landscape", x=0.05, y=0.05, xl=None, xr=None, yt=None, yb=None, start=None, end=None, tracklines=0, fragments=10, fragment_size=None, track_size=0.75, cross_track_links=None, ): """Initialize. Arguments: - parent Diagram object containing the data that the drawer draws - pagesize String describing the ISO size of the image, or a tuple of pixels - orientation String describing the required orientation of the final drawing ('landscape' or 'portrait') - x Float (0->1) describing the relative size of the X margins to the page - y Float (0->1) describing the relative size of the Y margins to the page - xl Float (0->1) describing the relative size of the left X margin to the page (overrides x) - xl Float (0->1) describing the relative size of the left X margin to the page (overrides x) - xr Float (0->1) describing the relative size of the right X margin to the page (overrides x) - yt Float (0->1) describing the relative size of the top Y margin to the page (overrides y) - yb Float (0->1) describing the relative size of the lower Y margin to the page (overrides y) - start Int, the position to begin drawing the diagram at - end Int, the position to stop drawing the diagram at - tracklines Boolean flag to show (or not) lines delineating tracks on the diagram - fragments Int, the number of equal fragments into which the sequence should be divided for drawing - fragment_size Float(0->1) The proportion of the available height for the fragment that should be taken up in drawing - track_size The proportion of the available track height that should be taken up in drawing - cross_track_links List of tuples each with four entries (track A, feature A, track B, feature B) to be linked. """ # Use the superclass' instantiation method AbstractDrawer.__init__( self, parent, pagesize, orientation, x, y, xl, xr, yt, yb, start, end, tracklines, cross_track_links, ) # Useful measurements on the page self.fragments = fragments if fragment_size is not None: self.fragment_size = fragment_size else: if self.fragments == 1: # For single fragments, default to full height self.fragment_size = 1 else: # Otherwise keep a 10% gap between fragments self.fragment_size = 0.9 self.track_size = track_size def draw(self): """Draw a linear diagram of the data in the parent Diagram object.""" # Instantiate the drawing canvas self.drawing = Drawing(self.pagesize[0], self.pagesize[1]) feature_elements = [] # holds feature elements feature_labels = [] # holds feature labels greytrack_bgs = [] # holds track background greytrack_labels = [] # holds track foreground labels scale_axes = [] # holds scale axes scale_labels = [] # holds scale axis labels # Get the tracks to be drawn self.drawn_tracks = self._parent.get_drawn_levels() # Set fragment and track sizes self.init_fragments() self.set_track_heights() # Go through each track in the parent (if it is to be drawn) one by # one and collate the data as drawing elements for track_level in self.drawn_tracks: # only use tracks to be drawn self.current_track_level = track_level # establish track level track = self._parent[track_level] # get the track at that level gbgs, glabels = self.draw_greytrack(track) # get greytrack elements greytrack_bgs.append(gbgs) greytrack_labels.append(glabels) features, flabels = self.draw_track(track) # get feature and graph elements feature_elements.append(features) feature_labels.append(flabels) if track.scale: axes, slabels = self.draw_scale(track) # get scale elements scale_axes.append(axes) scale_labels.append(slabels) feature_cross_links = [] for cross_link_obj in self.cross_track_links: cross_link_elements = self.draw_cross_link(cross_link_obj) if cross_link_elements: feature_cross_links.append(cross_link_elements) # Groups listed in order of addition to page (from back to front) # Draw track backgrounds # Draw feature cross track links # Draw features and graphs # Draw scale axes # Draw scale labels # Draw feature labels # Draw track labels element_groups = [ greytrack_bgs, feature_cross_links, feature_elements, scale_axes, scale_labels, feature_labels, greytrack_labels, ] for element_group in element_groups: for element_list in element_group: [self.drawing.add(element) for element in element_list] if self.tracklines: # Draw test tracks over top of diagram self.draw_test_tracks() def init_fragments(self): """Initialize useful values for positioning diagram elements.""" # Set basic heights, lengths etc self.fragment_height = self.pageheight / self.fragments # total fragment height in pixels self.fragment_bases = ceil(self.length / self.fragments) # fragment length in bases # Key fragment base and top lines by fragment number # Holds bottom and top line locations of fragments, keyed by fragment number self.fragment_lines = {} # Number of pixels to crop the fragment: fragment_crop = (1 - self.fragment_size) / 2 fragy = self.ylim # Holder for current absolute fragment base for fragment in range(self.fragments): fragtop = fragy - fragment_crop * self.fragment_height # top - crop fragbtm = ( fragy - (1 - fragment_crop) * self.fragment_height ) # bottom + crop self.fragment_lines[fragment] = (fragbtm, fragtop) fragy -= self.fragment_height # next fragment base # Key base starts and ends for each fragment by fragment number self.fragment_limits = {} # Holds first and last base positions in a fragment fragment_step = self.fragment_bases # bases per fragment fragment_count = 0 # Add start and end positions for each fragment to dictionary for marker in range(int(self.start), int(self.end), int(fragment_step)): self.fragment_limits[fragment_count] = (marker, marker + fragment_step) fragment_count += 1 def set_track_heights(self): """Set track heights. Since tracks may not be of identical heights, the bottom and top offsets of each track relative to the fragment top and bottom is stored in a dictionary - self.track_offsets, keyed by track number. """ bot_track = min(min(self.drawn_tracks), 1) top_track = max(self.drawn_tracks) # The 'highest' track number to draw trackunit_sum = 0 # Total number of 'units' for the tracks trackunits = {} # The start and end units for each track, keyed by track number heightholder = 0 # placeholder variable for track in range(bot_track, top_track + 1): # for all track numbers to 'draw' try: trackheight = self._parent[track].height # Get track height except Exception: # TODO: IndexError? trackheight = 1 # ...or default to 1 trackunit_sum += trackheight # increment total track unit height trackunits[track] = (heightholder, heightholder + trackheight) heightholder += trackheight # move to next height trackunit_height = self.fragment_height * self.fragment_size / trackunit_sum # Calculate top and bottom offsets for each track, relative to fragment # base track_offsets = {} # The offsets from fragment base for each track track_crop = ( trackunit_height * (1 - self.track_size) / 2.0 ) # 'step back' in pixels assert track_crop >= 0 for track in trackunits: top = trackunits[track][1] * trackunit_height - track_crop # top offset btm = trackunits[track][0] * trackunit_height + track_crop # bottom offset ctr = btm + (top - btm) / 2.0 # center offset track_offsets[track] = (btm, ctr, top) self.track_offsets = track_offsets def draw_test_tracks(self): """Draw test tracks. Draw red lines indicating the top and bottom of each fragment, and blue ones indicating tracks to be drawn. """ # Add lines for each fragment for fbtm, ftop in self.fragment_lines.values(): self.drawing.add( Line(self.x0, ftop, self.xlim, ftop, strokeColor=colors.red) ) # top line self.drawing.add( Line(self.x0, fbtm, self.xlim, fbtm, strokeColor=colors.red) ) # bottom line # Add track lines for this fragment - but only for drawn tracks for track in self.drawn_tracks: trackbtm = fbtm + self.track_offsets[track][0] trackctr = fbtm + self.track_offsets[track][1] tracktop = fbtm + self.track_offsets[track][2] self.drawing.add( Line( self.x0, tracktop, self.xlim, tracktop, strokeColor=colors.blue ) ) # top line self.drawing.add( Line( self.x0, trackctr, self.xlim, trackctr, strokeColor=colors.green ) ) # center line self.drawing.add( Line( self.x0, trackbtm, self.xlim, trackbtm, strokeColor=colors.blue ) ) # bottom line def draw_track(self, track): """Draw track. Arguments: - track Track object Returns a tuple (list of elements in the track, list of labels in the track). """ track_elements = [] # Holds elements from features and graphs track_labels = [] # Holds labels from features and graphs # Distribution dictionary for dealing with different set types set_methods = {FeatureSet: self.draw_feature_set, GraphSet: self.draw_graph_set} for set in track.get_sets(): # Draw the feature or graph sets elements, labels = set_methods[set.__class__](set) track_elements += elements track_labels += labels return track_elements, track_labels def draw_tick(self, tickpos, ctr, ticklen, track, draw_label): """Draw tick. Arguments: - tickpos Int, position of the tick on the sequence - ctr Float, Y co-ord of the center of the track - ticklen How long to draw the tick - track Track, the track the tick is drawn on - draw_label Boolean, write the tick label? Returns a drawing element that is the tick on the scale """ if self.start >= tickpos and tickpos >= self.end: raise RuntimeError( "Tick at %i, but showing %i to %i" % (tickpos, self.start, self.end) ) if not ( (track.start is None or track.start <= tickpos) and (track.end is None or tickpos <= track.end) ): raise RuntimeError( "Tick at %i, but showing %r to %r for track" % (tickpos, track.start, track.end) ) fragment, tickx = self.canvas_location(tickpos) # Tick coordinates assert fragment >= 0, "Fragment %i, tickpos %i" % (fragment, tickpos) tctr = ctr + self.fragment_lines[fragment][0] # Center line of the track tickx += self.x0 # Tick X co-ord ticktop = tctr + ticklen # Y co-ord of tick top tick = Line(tickx, tctr, tickx, ticktop, strokeColor=track.scale_color) if draw_label: # Put tick position on as label if track.scale_format == "SInt": if tickpos >= 1000000: tickstring = str(tickpos // 1000000) + " Mbp" elif tickpos >= 1000: tickstring = str(tickpos // 1000) + " Kbp" else: tickstring = str(tickpos) else: tickstring = str(tickpos) label = String( 0, 0, tickstring, # Make label string fontName=track.scale_font, fontSize=track.scale_fontsize, fillColor=track.scale_color, ) labelgroup = Group(label) rotation = angle2trig(track.scale_fontangle) labelgroup.transform = ( rotation[0], rotation[1], rotation[2], rotation[3], tickx, ticktop, ) else: labelgroup = None return tick, labelgroup def draw_scale(self, track): """Draw scale. Argument: - track Track object Returns a tuple of (list of elements in the scale, list of labels in the scale). """ scale_elements = [] # Holds axes and ticks scale_labels = [] # Holds labels if not track.scale: # No scale required, exit early return [], [] # Get track location btm, ctr, top = self.track_offsets[self.current_track_level] trackheight = top - ctr # For each fragment, draw the scale for this track start, end = self._current_track_start_end() start_f, start_x = self.canvas_location(start) end_f, end_x = self.canvas_location(end) for fragment in range(start_f, end_f + 1): tbtm = btm + self.fragment_lines[fragment][0] tctr = ctr + self.fragment_lines[fragment][0] ttop = top + self.fragment_lines[fragment][0] # X-axis if fragment == start_f: x_left = start_x else: x_left = 0 if fragment == end_f: x_right = end_x # Y-axis end marker scale_elements.append( Line( self.x0 + x_right, tbtm, self.x0 + x_right, ttop, strokeColor=track.scale_color, ) ) else: x_right = self.xlim - self.x0 scale_elements.append( Line( self.x0 + x_left, tctr, self.x0 + x_right, tctr, strokeColor=track.scale_color, ) ) # Y-axis start marker scale_elements.append( Line( self.x0 + x_left, tbtm, self.x0 + x_left, ttop, strokeColor=track.scale_color, ) ) start, end = self._current_track_start_end() if track.scale_ticks: # Ticks are required on the scale # Draw large ticks # I want the ticks to be consistently positioned relative to # the start of the sequence (position 0), not relative to the # current viewpoint (self.start and self.end) ticklen = track.scale_largeticks * trackheight tickiterval = int(track.scale_largetick_interval) # Note that we could just start the list of ticks using # range(0,self.end,tickinterval) and the filter out the # ones before self.start - but this seems wasteful. # Using tickiterval * (self.start//tickiterval) is a shortcut. for tickpos in range( tickiterval * (self.start // tickiterval), int(self.end), tickiterval ): if tickpos <= start or end <= tickpos: continue tick, label = self.draw_tick( tickpos, ctr, ticklen, track, track.scale_largetick_labels ) scale_elements.append(tick) if label is not None: # If there's a label, add it scale_labels.append(label) # Draw small ticks ticklen = track.scale_smallticks * trackheight tickiterval = int(track.scale_smalltick_interval) for tickpos in range( tickiterval * (self.start // tickiterval), int(self.end), tickiterval ): if tickpos <= start or end <= tickpos: continue tick, label = self.draw_tick( tickpos, ctr, ticklen, track, track.scale_smalltick_labels ) scale_elements.append(tick) if label is not None: # If there's a label, add it scale_labels.append(label) # Check to see if the track contains a graph - if it does, get the # minimum and maximum values, and put them on the scale Y-axis if track.axis_labels: for set in track.get_sets(): # Check all sets... if set.__class__ is GraphSet: # ...for a graph set graph_label_min = [] graph_label_mid = [] graph_label_max = [] for graph in set.get_graphs(): quartiles = graph.quartiles() minval, maxval = quartiles[0], quartiles[4] if graph.center is None: midval = (maxval + minval) / 2.0 graph_label_min.append(f"{minval:.3f}") graph_label_max.append(f"{maxval:.3f}") else: diff = max((graph.center - minval), (maxval - graph.center)) minval = graph.center - diff maxval = graph.center + diff midval = graph.center graph_label_mid.append(f"{midval:.3f}") graph_label_min.append(f"{minval:.3f}") graph_label_max.append(f"{maxval:.3f}") for fragment in range( start_f, end_f + 1 ): # Add to all used fragment axes tbtm = btm + self.fragment_lines[fragment][0] tctr = ctr + self.fragment_lines[fragment][0] ttop = top + self.fragment_lines[fragment][0] if fragment == start_f: x_left = start_x else: x_left = 0 for val, pos in [ (";".join(graph_label_min), tbtm), (";".join(graph_label_max), ttop), (";".join(graph_label_mid), tctr), ]: label = String( 0, 0, val, fontName=track.scale_font, fontSize=track.scale_fontsize, fillColor=track.scale_color, ) labelgroup = Group(label) rotation = angle2trig(track.scale_fontangle) labelgroup.transform = ( rotation[0], rotation[1], rotation[2], rotation[3], self.x0 + x_left, pos, ) scale_labels.append(labelgroup) return scale_elements, scale_labels def draw_greytrack(self, track): """Draw greytrack. Arguments: - track Track object Put in a grey background to the current track in all fragments, if track specifies that we should. """ greytrack_bgs = [] # Holds grey track backgrounds greytrack_labels = [] # Holds grey foreground labels if not track.greytrack: # No greytrack required, return early return [], [] # Get track location btm, ctr, top = self.track_offsets[self.current_track_level] start, end = self._current_track_start_end() start_fragment, start_offset = self.canvas_location(start) end_fragment, end_offset = self.canvas_location(end) # Add greytrack to all fragments for this track for fragment in range(start_fragment, end_fragment + 1): tbtm = btm + self.fragment_lines[fragment][0] tctr = ctr + self.fragment_lines[fragment][0] ttop = top + self.fragment_lines[fragment][0] if fragment == start_fragment: x1 = self.x0 + start_offset else: x1 = self.x0 if fragment == end_fragment: x2 = self.x0 + end_offset else: x2 = self.xlim box = draw_box( (x1, tbtm), (x2, ttop), colors.Color(0.96, 0.96, 0.96), # Grey track bg ) # is just a box greytrack_bgs.append(box) if track.greytrack_labels: # If labels are required # # how far apart should they be? labelstep = self.pagewidth / track.greytrack_labels label = String( 0, 0, track.name, # label contents fontName=track.greytrack_font, fontSize=track.greytrack_fontsize, fillColor=track.greytrack_fontcolor, ) # Create a new labelgroup at each position the label is required for x in range(int(self.x0), int(self.xlim), int(labelstep)): if fragment == start_fragment and x < start_offset: continue if ( fragment == end_fragment and end_offset < x + label.getBounds()[2] ): continue labelgroup = Group(label) rotation = angle2trig(track.greytrack_font_rotation) labelgroup.transform = ( rotation[0], rotation[1], rotation[2], rotation[3], x, tbtm, ) if not self.xlim - x <= labelstep: # Don't overlap the end of the track greytrack_labels.append(labelgroup) return greytrack_bgs, greytrack_labels def draw_feature_set(self, set): """Draw feature set. Arguments: - set FeatureSet object Returns a tuple (list of elements describing features, list of labels for elements). """ # print("draw feature set") feature_elements = [] # Holds diagram elements belonging to the features label_elements = [] # Holds diagram elements belonging to feature labels # Collect all the elements for the feature set for feature in set.get_features(): if self.is_in_bounds(feature.start) or self.is_in_bounds(feature.end): features, labels = self.draw_feature(feature) # get elements and labels feature_elements += features label_elements += labels return feature_elements, label_elements def draw_feature(self, feature): """Draw feature. Arguments: - feature Feature containing location info Returns tuple of (list of elements describing single feature, list of labels for those elements). """ if feature.hide: # Feature hidden, don't draw it... return [], [] feature_elements = [] # Holds diagram elements belonging to the feature label_elements = [] # Holds labels belonging to the feature start, end = self._current_track_start_end() # A single feature may be split into subfeatures, so loop over them for locstart, locend in feature.locations: if locend < start: continue locstart = max(locstart, start) if end < locstart: continue locend = min(locend, end) feature_boxes = self.draw_feature_location(feature, locstart, locend) for box, label in feature_boxes: feature_elements.append(box) if label is not None: label_elements.append(label) return feature_elements, label_elements def draw_feature_location(self, feature, locstart, locend): """Draw feature location.""" feature_boxes = [] # Get start and end positions for feature/subfeatures start_fragment, start_offset = self.canvas_location(locstart) end_fragment, end_offset = self.canvas_location(locend) # print("start_fragment, start_offset", start_fragment, start_offset) # print("end_fragment, end_offset", end_fragment, end_offset) # print("start, end", locstart, locend) # Note that there is a strange situation where a feature may be in # several parts, and one or more of those parts may end up being # drawn on a non-existent fragment. So we check that the start and # end fragments do actually exist in terms of the drawing allowed_fragments = list(self.fragment_limits.keys()) if start_fragment in allowed_fragments and end_fragment in allowed_fragments: # print(feature.name, feature.start, feature.end, start_offset, end_offset) if start_fragment == end_fragment: # Feature is found on one fragment feature_box, label = self.get_feature_sigil( feature, start_offset, end_offset, start_fragment ) feature_boxes.append((feature_box, label)) # feature_elements.append(feature_box) # if label is not None: # There is a label for the feature # label_elements.append(label) else: # Feature is split over two or more fragments fragment = start_fragment start = start_offset # The bit that runs up to the end of the first fragment, # and any bits that subsequently span whole fragments while self.fragment_limits[fragment][1] < locend: # print(fragment, self.fragment_limits[fragment][1], locend) feature_box, label = self.get_feature_sigil( feature, start, self.pagewidth, fragment ) fragment += 1 # move to next fragment start = 0 # start next sigil from start of fragment feature_boxes.append((feature_box, label)) # feature_elements.append(feature_box) # if label is not None: # There's a label for the feature # label_elements.append(label) # The last bit of the feature # print(locend, self.end, fragment) # print(self.fragment_bases, self.length) feature_box, label = self.get_feature_sigil( feature, 0, end_offset, fragment ) feature_boxes.append((feature_box, label)) # if locstart > locend: # print(locstart, locend, feature.location.strand, feature_boxes, feature.name) return feature_boxes def draw_cross_link(self, cross_link): """Draw cross-link between two features.""" startA = cross_link.startA startB = cross_link.startB endA = cross_link.endA endB = cross_link.endB if not self.is_in_bounds(startA) and not self.is_in_bounds(endA): return None if not self.is_in_bounds(startB) and not self.is_in_bounds(endB): return None if startA < self.start: startA = self.start if startB < self.start: startB = self.start if self.end < endA: endA = self.end if self.end < endB: endB = self.end trackobjA = cross_link._trackA(list(self._parent.tracks.values())) trackobjB = cross_link._trackB(list(self._parent.tracks.values())) assert trackobjA is not None assert trackobjB is not None if trackobjA == trackobjB: raise NotImplementedError if trackobjA.start is not None: if endA < trackobjA.start: return startA = max(startA, trackobjA.start) if trackobjA.end is not None: if trackobjA.end < startA: return endA = min(endA, trackobjA.end) if trackobjB.start is not None: if endB < trackobjB.start: return startB = max(startB, trackobjB.start) if trackobjB.end is not None: if trackobjB.end < startB: return endB = min(endB, trackobjB.end) for track_level in self._parent.get_drawn_levels(): track = self._parent[track_level] if track == trackobjA: trackA = track_level if track == trackobjB: trackB = track_level if trackA == trackB: raise NotImplementedError strokecolor, fillcolor = _stroke_and_fill_colors( cross_link.color, cross_link.border ) allowed_fragments = list(self.fragment_limits.keys()) start_fragmentA, start_offsetA = self.canvas_location(startA) end_fragmentA, end_offsetA = self.canvas_location(endA) if ( start_fragmentA not in allowed_fragments or end_fragmentA not in allowed_fragments ): return start_fragmentB, start_offsetB = self.canvas_location(startB) end_fragmentB, end_offsetB = self.canvas_location(endB) if ( start_fragmentB not in allowed_fragments or end_fragmentB not in allowed_fragments ): return # TODO - Better drawing of flips when split between fragments answer = [] for fragment in range( min(start_fragmentA, start_fragmentB), max(end_fragmentA, end_fragmentB) + 1 ): btmA, ctrA, topA = self.track_offsets[trackA] btmA += self.fragment_lines[fragment][0] ctrA += self.fragment_lines[fragment][0] topA += self.fragment_lines[fragment][0] btmB, ctrB, topB = self.track_offsets[trackB] btmB += self.fragment_lines[fragment][0] ctrB += self.fragment_lines[fragment][0] topB += self.fragment_lines[fragment][0] if self.fragment_limits[fragment][1] < endA: xAe = self.x0 + self.pagewidth crop_rightA = True else: xAe = self.x0 + end_offsetA crop_rightA = False if self.fragment_limits[fragment][1] < endB: xBe = self.x0 + self.pagewidth crop_rightB = True else: xBe = self.x0 + end_offsetB crop_rightB = False if fragment < start_fragmentA: xAs = self.x0 + self.pagewidth xAe = xAs crop_leftA = False elif fragment == start_fragmentA: xAs = self.x0 + start_offsetA crop_leftA = False else: xAs = self.x0 crop_leftA = True if fragment < start_fragmentB: xBs = self.x0 + self.pagewidth xBe = xBs crop_leftB = False elif fragment == start_fragmentB: xBs = self.x0 + start_offsetB crop_leftB = False else: xBs = self.x0 crop_leftB = True if ctrA < ctrB: yA = topA yB = btmB else: yA = btmA yB = topB if fragment < start_fragmentB or end_fragmentB < fragment: if cross_link.flip: # Just draw A as a triangle to left/right if fragment < start_fragmentB: extra = [self.x0 + self.pagewidth, 0.5 * (yA + yB)] else: extra = [self.x0, 0.5 * (yA + yB)] else: if fragment < start_fragmentB: extra = [ self.x0 + self.pagewidth, 0.7 * yA + 0.3 * yB, self.x0 + self.pagewidth, 0.3 * yA + 0.7 * yB, ] else: extra = [ self.x0, 0.3 * yA + 0.7 * yB, self.x0, 0.7 * yA + 0.3 * yB, ] answer.append( Polygon( deduplicate([xAs, yA, xAe, yA] + extra), strokeColor=strokecolor, fillColor=fillcolor, # default is mitre/miter which can stick out too much: strokeLineJoin=1, # 1=round strokewidth=0, ) ) elif fragment < start_fragmentA or end_fragmentA < fragment: if cross_link.flip: # Just draw B as a triangle to left if fragment < start_fragmentA: extra = [self.x0 + self.pagewidth, 0.5 * (yA + yB)] else: extra = [self.x0, 0.5 * (yA + yB)] else: if fragment < start_fragmentA: extra = [ self.x0 + self.pagewidth, 0.3 * yA + 0.7 * yB, self.x0 + self.pagewidth, 0.7 * yA + 0.3 * yB, ] else: extra = [ self.x0, 0.7 * yA + 0.3 * yB, self.x0, 0.3 * yA + 0.7 * yB, ] answer.append( Polygon( deduplicate([xBs, yB, xBe, yB] + extra), strokeColor=strokecolor, fillColor=fillcolor, # default is mitre/miter which can stick out too much: strokeLineJoin=1, # 1=round strokewidth=0, ) ) elif cross_link.flip and ( (crop_leftA and not crop_rightA) or (crop_leftB and not crop_rightB) ): # On left end of fragment... force "crossing" to margin answer.append( Polygon( deduplicate( [ xAs, yA, xAe, yA, self.x0, 0.5 * (yA + yB), xBe, yB, xBs, yB, ] ), strokeColor=strokecolor, fillColor=fillcolor, # default is mitre/miter which can stick out too much: strokeLineJoin=1, # 1=round strokewidth=0, ) ) elif cross_link.flip and ( (crop_rightA and not crop_leftA) or (crop_rightB and not crop_leftB) ): # On right end... force "crossing" to margin answer.append( Polygon( deduplicate( [ xAs, yA, xAe, yA, xBe, yB, xBs, yB, self.x0 + self.pagewidth, 0.5 * (yA + yB), ] ), strokeColor=strokecolor, fillColor=fillcolor, # default is mitre/miter which can stick out too much: strokeLineJoin=1, # 1=round strokewidth=0, ) ) elif cross_link.flip: answer.append( Polygon( deduplicate([xAs, yA, xAe, yA, xBs, yB, xBe, yB]), strokeColor=strokecolor, fillColor=fillcolor, # default is mitre/miter which can stick out too much: strokeLineJoin=1, # 1=round strokewidth=0, ) ) else: answer.append( Polygon( deduplicate([xAs, yA, xAe, yA, xBe, yB, xBs, yB]), strokeColor=strokecolor, fillColor=fillcolor, # default is mitre/miter which can stick out too much: strokeLineJoin=1, # 1=round strokewidth=0, ) ) return answer def get_feature_sigil(self, feature, x0, x1, fragment, **kwargs): """Get feature sigil. Arguments: - feature Feature object - x0 Start X coordinate on diagram - x1 End X coordinate on diagram - fragment The fragment on which the feature appears Returns a drawable indicator of the feature, and any required label for it. """ # Establish coordinates for drawing x0, x1 = self.x0 + x0, self.x0 + x1 btm, ctr, top = self.track_offsets[self.current_track_level] try: btm += self.fragment_lines[fragment][0] ctr += self.fragment_lines[fragment][0] top += self.fragment_lines[fragment][0] except Exception: # Only called if the method screws up big time print("We've got a screw-up") print(f"{self.start} {self.end}") print(self.fragment_bases) print(f"{x0!r} {x1!r}") for locstart, locend in feature.locations: print(self.canvas_location(locstart)) print(self.canvas_location(locend)) print(f"FEATURE\n{feature}") raise # Distribution dictionary for various ways of drawing the feature draw_methods = { "BOX": self._draw_sigil_box, "ARROW": self._draw_sigil_arrow, "BIGARROW": self._draw_sigil_big_arrow, "OCTO": self._draw_sigil_octo, "JAGGY": self._draw_sigil_jaggy, } method = draw_methods[feature.sigil] kwargs["head_length_ratio"] = feature.arrowhead_length kwargs["shaft_height_ratio"] = feature.arrowshaft_height # Support for clickable links... needs ReportLab 2.4 or later # which added support for links in SVG output. if hasattr(feature, "url"): kwargs["hrefURL"] = feature.url kwargs["hrefTitle"] = feature.name # Get sigil for the feature, give it the bounding box straddling # the axis (it decides strand specific placement) sigil = method( btm, ctr, top, x0, x1, strand=feature.location.strand, color=feature.color, border=feature.border, **kwargs, ) if feature.label_strand: strand = feature.label_strand else: strand = feature.location.strand if feature.label: # Feature requires a label label = String( 0, 0, feature.name, fontName=feature.label_font, fontSize=feature.label_size, fillColor=feature.label_color, ) labelgroup = Group(label) # Feature is on top, or covers both strands (location affects # the height and rotation of the label) if strand != -1: rotation = angle2trig(feature.label_angle) if feature.label_position in ("end", "3'", "right"): pos = x1 elif feature.label_position in ("middle", "center", "centre"): pos = (x1 + x0) / 2.0 else: # Default to start, i.e. 'start', "5'", 'left' pos = x0 labelgroup.transform = ( rotation[0], rotation[1], rotation[2], rotation[3], pos, top, ) else: # Feature on bottom strand rotation = angle2trig(feature.label_angle + 180) if feature.label_position in ("end", "3'", "right"): pos = x0 elif feature.label_position in ("middle", "center", "centre"): pos = (x1 + x0) / 2.0 else: # Default to start, i.e. 'start', "5'", 'left' pos = x1 labelgroup.transform = ( rotation[0], rotation[1], rotation[2], rotation[3], pos, btm, ) else: labelgroup = None return sigil, labelgroup def draw_graph_set(self, set): """Draw graph set. Arguments: - set GraphSet object Returns tuple (list of graph elements, list of graph labels). """ # print('draw graph set') elements = [] # Holds graph elements # Distribution dictionary for how to draw the graph style_methods = { "line": self.draw_line_graph, "heat": self.draw_heat_graph, "bar": self.draw_bar_graph, } for graph in set.get_graphs(): elements += style_methods[graph.style](graph) return elements, [] def draw_line_graph(self, graph): """Return a line graph as a list of drawable elements. Arguments: - graph Graph object """ # print('\tdraw_line_graph') line_elements = [] # Holds drawable elements # Get graph data data_quartiles = graph.quartiles() minval, maxval = data_quartiles[0], data_quartiles[4] btm, ctr, top = self.track_offsets[self.current_track_level] trackheight = 0.5 * (top - btm) datarange = maxval - minval if datarange == 0: datarange = trackheight start, end = self._current_track_start_end() data = graph[start:end] # midval is the value at which the x-axis is plotted, and is the # central ring in the track if graph.center is None: midval = (maxval + minval) / 2.0 else: midval = graph.center # Whichever is the greatest difference: max-midval or min-midval, is # taken to specify the number of pixel units resolved along the # y-axis resolution = max((midval - minval), (maxval - midval)) # Start from first data point pos, val = data[0] lastfrag, lastx = self.canvas_location(pos) lastx += self.x0 # Start xy co-ords lasty = ( trackheight * (val - midval) / resolution + self.fragment_lines[lastfrag][0] + ctr ) lastval = val # Add a series of lines linking consecutive data points for pos, val in data: frag, x = self.canvas_location(pos) x += self.x0 # next xy co-ords y = ( trackheight * (val - midval) / resolution + self.fragment_lines[frag][0] + ctr ) if frag == lastfrag: # Points on the same fragment: draw the line line_elements.append( Line( lastx, lasty, x, y, strokeColor=graph.poscolor, strokeWidth=graph.linewidth, ) ) else: # Points not on the same fragment, so interpolate tempy = ( trackheight * (val - midval) / resolution + self.fragment_lines[lastfrag][0] + ctr ) line_elements.append( Line( lastx, lasty, self.xlim, tempy, strokeColor=graph.poscolor, strokeWidth=graph.linewidth, ) ) tempy = ( trackheight * (val - midval) / resolution + self.fragment_lines[frag][0] + ctr ) line_elements.append( Line( self.x0, tempy, x, y, strokeColor=graph.poscolor, strokeWidth=graph.linewidth, ) ) lastfrag, lastx, lasty, lastval = frag, x, y, val return line_elements def draw_heat_graph(self, graph): """Return a list of drawable elements for the heat graph.""" # print('\tdraw_heat_graph') # At each point contained in the graph data, we draw a box that is the # full height of the track, extending from the midpoint between the # previous and current data points to the midpoint between the current # and next data points heat_elements = [] # Holds drawable elements for the graph # Get graph data and information data_quartiles = graph.quartiles() minval, maxval = data_quartiles[0], data_quartiles[4] midval = (maxval + minval) / 2.0 # mid is the value at the X-axis btm, ctr, top = self.track_offsets[self.current_track_level] trackheight = top - btm start, end = self._current_track_start_end() data = intermediate_points(start, end, graph[start:end]) if not data: return [] # Create elements on the graph, indicating a large positive value by # the graph's poscolor, and a large negative value by the graph's # negcolor attributes for pos0, pos1, val in data: # assert start <= pos0 <= pos1 <= end fragment0, x0 = self.canvas_location(pos0) fragment1, x1 = self.canvas_location(pos1) x0, x1 = self.x0 + x0, self.x0 + x1 # account for margin # print('x1 before:', x1) # Calculate the heat color, based on the differential between # the value and the median value heat = colors.linearlyInterpolatedColor( graph.poscolor, graph.negcolor, maxval, minval, val ) # Draw heat box if fragment0 == fragment1: # Box is contiguous on one fragment if pos1 >= self.fragment_limits[fragment0][1]: x1 = self.xlim ttop = top + self.fragment_lines[fragment0][0] tbtm = btm + self.fragment_lines[fragment0][0] # print('equal', pos0, pos1, val) # print(pos0, pos1, fragment0, fragment1) heat_elements.append( draw_box((x0, tbtm), (x1, ttop), color=heat, border=None) ) else: # box is split over two or more fragments # if pos0 >= self.fragment_limits[fragment0][0]: # fragment0 += 1 fragment = fragment0 start_x = x0 while self.fragment_limits[fragment][1] <= pos1: # print(pos0, self.fragment_limits[fragment][1], pos1) ttop = top + self.fragment_lines[fragment][0] tbtm = btm + self.fragment_lines[fragment][0] heat_elements.append( draw_box( (start_x, tbtm), (self.xlim, ttop), color=heat, border=None ) ) fragment += 1 start_x = self.x0 ttop = top + self.fragment_lines[fragment][0] tbtm = btm + self.fragment_lines[fragment][0] # Add the last part of the bar # print('x1 after:', x1, '\n') heat_elements.append( draw_box((self.x0, tbtm), (x1, ttop), color=heat, border=None) ) return heat_elements def draw_bar_graph(self, graph): """Return list of drawable elements for a bar graph.""" # print('\tdraw_bar_graph') # At each point contained in the graph data, we draw a vertical bar # from the track center to the height of the datapoint value (positive # values go up in one color, negative go down in the alternative # color). bar_elements = [] # Holds drawable elements for the graph # Set the number of pixels per unit for the data data_quartiles = graph.quartiles() minval, maxval = data_quartiles[0], data_quartiles[4] btm, ctr, top = self.track_offsets[self.current_track_level] trackheight = 0.5 * (top - btm) datarange = maxval - minval if datarange == 0: datarange = trackheight data = graph[self.start : self.end] # midval is the value at which the x-axis is plotted, and is the # central ring in the track if graph.center is None: midval = (maxval + minval) / 2.0 else: midval = graph.center # Convert data into 'binned' blocks, covering half the distance to the # next data point on either side, accounting for the ends of fragments # and tracks start, end = self._current_track_start_end() data = intermediate_points(start, end, graph[start:end]) if not data: return [] # Whichever is the greatest difference: max-midval or min-midval, is # taken to specify the number of pixel units resolved along the # y-axis resolution = max((midval - minval), (maxval - midval)) if resolution == 0: resolution = trackheight # Create elements for the bar graph based on newdata for pos0, pos1, val in data: fragment0, x0 = self.canvas_location(pos0) fragment1, x1 = self.canvas_location(pos1) x0, x1 = self.x0 + x0, self.x0 + x1 # account for margin barval = trackheight * (val - midval) / resolution if barval >= 0: # Different colors for bars that extend above... barcolor = graph.poscolor else: # ...or below the axis barcolor = graph.negcolor # Draw bar if fragment0 == fragment1: # Box is contiguous if pos1 >= self.fragment_limits[fragment0][1]: x1 = self.xlim tctr = ctr + self.fragment_lines[fragment0][0] barval += tctr bar_elements.append(draw_box((x0, tctr), (x1, barval), color=barcolor)) else: # Box is split over two or more fragments fragment = fragment0 # if pos0 >= self.fragment_limits[fragment0][0]: # fragment += 1 start = x0 while self.fragment_limits[fragment][1] < pos1: tctr = ctr + self.fragment_lines[fragment][0] thisbarval = barval + tctr bar_elements.append( draw_box((start, tctr), (self.xlim, thisbarval), color=barcolor) ) fragment += 1 start = self.x0 tctr = ctr + self.fragment_lines[fragment1][0] barval += tctr # Add the last part of the bar bar_elements.append( draw_box((self.x0, tctr), (x1, barval), color=barcolor) ) return bar_elements def canvas_location(self, base): """Canvas location of a base on the genome. Arguments: - base The base number on the genome sequence Returns the x-coordinate and fragment number of a base on the genome sequence, in the context of the current drawing setup """ base = int(base - self.start) # number of bases we are from the start fragment = int(base / self.fragment_bases) if fragment < 1: # First fragment base_offset = base fragment = 0 elif fragment >= self.fragments: fragment = self.fragments - 1 base_offset = self.fragment_bases else: # Calculate number of bases from start of fragment base_offset = base % self.fragment_bases assert fragment < self.fragments, ( base, self.start, self.end, self.length, self.fragment_bases, ) # Calculate number of pixels from start of fragment x_offset = self.pagewidth * base_offset / self.fragment_bases return fragment, x_offset def _draw_sigil_box(self, bottom, center, top, x1, x2, strand, **kwargs): """Draw BOX sigil (PRIVATE).""" if strand == 1: y1 = center y2 = top elif strand == -1: y1 = bottom y2 = center else: y1 = bottom y2 = top return draw_box((x1, y1), (x2, y2), **kwargs) def _draw_sigil_octo(self, bottom, center, top, x1, x2, strand, **kwargs): """Draw OCTO sigil, a box with the corners cut off (PRIVATE).""" if strand == 1: y1 = center y2 = top elif strand == -1: y1 = bottom y2 = center else: y1 = bottom y2 = top return draw_cut_corner_box((x1, y1), (x2, y2), **kwargs) def _draw_sigil_jaggy( self, bottom, center, top, x1, x2, strand, color, border=None, **kwargs ): """Draw JAGGY sigil (PRIVATE). Although we may in future expose the head/tail jaggy lengths, for now both the left and right edges are drawn jagged. """ if strand == 1: y1 = center y2 = top teeth = 2 elif strand == -1: y1 = bottom y2 = center teeth = 2 else: y1 = bottom y2 = top teeth = 4 xmin = min(x1, x2) xmax = max(x1, x2) height = y2 - y1 boxwidth = x2 - x1 tooth_length = min(height / teeth, boxwidth * 0.5) headlength = tooth_length taillength = tooth_length strokecolor, color = _stroke_and_fill_colors(color, border) points = [] for i in range(teeth): points.extend( ( xmin, y1 + i * height / teeth, xmin + taillength, y1 + (i + 1) * height / teeth, ) ) for i in range(teeth): points.extend( ( xmax, y1 + (teeth - i) * height / teeth, xmax - headlength, y1 + (teeth - i - 1) * height / teeth, ) ) return Polygon( deduplicate(points), strokeColor=strokecolor, strokeWidth=1, strokeLineJoin=1, # 1=round fillColor=color, **kwargs, ) def _draw_sigil_arrow(self, bottom, center, top, x1, x2, strand, **kwargs): """Draw ARROW sigil (PRIVATE).""" if strand == 1: y1 = center y2 = top orientation = "right" elif strand == -1: y1 = bottom y2 = center orientation = "left" else: y1 = bottom y2 = top orientation = "right" # backward compatibility return draw_arrow((x1, y1), (x2, y2), orientation=orientation, **kwargs) def _draw_sigil_big_arrow(self, bottom, center, top, x1, x2, strand, **kwargs): """Draw BIGARROW sigil, like ARROW but straddles the axis (PRIVATE).""" if strand == -1: orientation = "left" else: orientation = "right" return draw_arrow((x1, bottom), (x2, top), orientation=orientation, **kwargs)