Package Bio :: Package Graphics :: Package GenomeDiagram :: Module _CircularDrawer
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Source Code for Module Bio.Graphics.GenomeDiagram._CircularDrawer

   1  # Copyright 2003-2008 by Leighton Pritchard.  All rights reserved. 
   2  # Revisions copyright 2008-2009 by Peter Cock. 
   3  # This code is part of the Biopython distribution and governed by its 
   4  # license.  Please see the LICENSE file that should have been included 
   5  # as part of this package. 
   6  # 
   7  # Contact:       Leighton Pritchard, Scottish Crop Research Institute, 
   8  #                Invergowrie, Dundee, Scotland, DD2 5DA, UK 
   9  #                L.Pritchard@scri.ac.uk 
  10  ################################################################################ 
  11   
  12  """ CircularDrawer module 
  13   
  14      Provides: 
  15   
  16      o CircularDrawer -  Drawing object for circular diagrams 
  17   
  18      For drawing capabilities, this module uses reportlab to draw and write 
  19      the diagram: 
  20   
  21      http://www.reportlab.com 
  22   
  23      For dealing with biological information, the package expects BioPython 
  24      objects: 
  25   
  26      http://www.biopython.org 
  27  """ 
  28   
  29  # ReportLab imports 
  30  from reportlab.graphics.shapes import * 
  31  from reportlab.lib import colors 
  32  from reportlab.pdfbase import _fontdata 
  33  from reportlab.graphics.shapes import ArcPath 
  34   
  35  # GenomeDiagram imports 
  36  from _AbstractDrawer import AbstractDrawer, draw_polygon, intermediate_points 
  37  from _FeatureSet import FeatureSet 
  38  from _GraphSet import GraphSet 
  39   
  40  from math import ceil, pi, cos, sin, asin 
  41   
42 -class CircularDrawer(AbstractDrawer):
43 """ CircularDrawer(AbstractDrawer) 44 45 Inherits from: 46 47 o AbstractDrawer 48 49 Provides: 50 51 Methods: 52 53 o __init__(self, parent=None, pagesize='A3', orientation='landscape', 54 x=0.05, y=0.05, xl=None, xr=None, yt=None, yb=None, 55 start=None, end=None, tracklines=0, track_size=0.75, 56 circular=1) Called on instantiation 57 58 o set_page_size(self, pagesize, orientation) Set the page size to the 59 passed size and orientation 60 61 o set_margins(self, x, y, xl, xr, yt, yb) Set the drawable area of the 62 page 63 64 o set_bounds(self, start, end) Set the bounds for the elements to be 65 drawn 66 67 o is_in_bounds(self, value) Returns a boolean for whether the position 68 is actually to be drawn 69 70 o __len__(self) Returns the length of sequence that will be drawn 71 72 73 o draw(self) Place the drawing elements on the diagram 74 75 o init_fragments(self) Calculate information 76 about sequence fragment locations on the drawing 77 78 o set_track_heights(self) Calculate information about the offset of 79 each track from the fragment base 80 81 o draw_test_tracks(self) Add lines demarcating each track to the 82 drawing 83 84 o draw_track(self, track) Return the contents of the passed track as 85 drawing elements 86 87 o draw_scale(self, track) Return a scale for the passed track as 88 drawing elements 89 90 o draw_greytrack(self, track) Return a grey background and superposed 91 label for the passed track as drawing 92 elements 93 94 o draw_feature_set(self, set) Return the features in the passed set as 95 drawing elements 96 97 o draw_feature(self, feature) Return a single feature as drawing 98 elements 99 100 o get_feature_sigil(self, feature, x0, x1, fragment) Return a single 101 feature as its sigil in drawing elements 102 103 o draw_graph_set(self, set) Return the data in a set of graphs as 104 drawing elements 105 106 o draw_line_graph(self, graph) Return the data in a graph as a line 107 graph in drawing elements 108 109 o draw_heat_graph(self, graph) Return the data in a graph as a heat 110 graph in drawing elements 111 112 o draw_bar_graph(self, graph) Return the data in a graph as a bar 113 graph in drawing elements 114 115 o canvas_angle(self, base) Return the angle, and cos and sin of 116 that angle, subtended by the passed 117 base position at the diagram center 118 119 o draw_arc(self, inner_radius, outer_radius, startangle, endangle, 120 color) Return a drawable element describing an arc 121 122 Attributes: 123 124 o tracklines Boolean for whether to draw lines dilineating tracks 125 126 o pagesize Tuple describing the size of the page in pixels 127 128 o x0 Float X co-ord for leftmost point of drawable area 129 130 o xlim Float X co-ord for rightmost point of drawable area 131 132 o y0 Float Y co-ord for lowest point of drawable area 133 134 o ylim Float Y co-ord for topmost point of drawable area 135 136 o pagewidth Float pixel width of drawable area 137 138 o pageheight Float pixel height of drawable area 139 140 o xcenter Float X co-ord of center of drawable area 141 142 o ycenter Float Y co-ord of center of drawable area 143 144 o start Int, base to start drawing from 145 146 o end Int, base to stop drawing at 147 148 o length Size of sequence to be drawn 149 150 o track_size Float (0->1) the proportion of the track height to 151 draw in 152 153 o drawing Drawing canvas 154 155 o drawn_tracks List of ints denoting which tracks are to be drawn 156 157 o current_track_level Int denoting which track is currently being 158 drawn 159 160 o track_offsets Dictionary of number of pixels that each track top, 161 center and bottom is offset from the base of a 162 fragment, keyed by track 163 164 o sweep Float (0->1) the proportion of the circle circumference to 165 use for the diagram 166 167 """
168 - def __init__(self, parent=None, pagesize='A3', orientation='landscape', 169 x=0.05, y=0.05, xl=None, xr=None, yt=None, yb=None, 170 start=None, end=None, tracklines=0, track_size=0.75, 171 circular=1):
172 """ __init__(self, parent, pagesize='A3', orientation='landscape', 173 x=0.05, y=0.05, xl=None, xr=None, yt=None, yb=None, 174 start=None, end=None, tracklines=0, track_size=0.75, 175 circular=1) 176 177 o parent Diagram object containing the data that the drawer 178 draws 179 180 o pagesize String describing the ISO size of the image, or a tuple 181 of pixels 182 183 o orientation String describing the required orientation of the 184 final drawing ('landscape' or 'portrait') 185 186 o x Float (0->1) describing the relative size of the X 187 margins to the page 188 189 o y Float (0->1) describing the relative size of the Y 190 margins to the page 191 192 o xl Float (0->1) describing the relative size of the left X 193 margin to the page (overrides x) 194 195 o xl Float (0->1) describing the relative size of the left X 196 margin to the page (overrides x) 197 198 o xr Float (0->1) describing the relative size of the right X 199 margin to the page (overrides x) 200 201 o yt Float (0->1) describing the relative size of the top Y 202 margin to the page (overrides y) 203 204 o yb Float (0->1) describing the relative size of the lower Y 205 margin to the page (overrides y) 206 207 o start Int, the position to begin drawing the diagram at 208 209 o end Int, the position to stop drawing the diagram at 210 211 o tracklines Boolean flag to show (or not) lines delineating tracks 212 on the diagram 213 214 o track_size The proportion of the available track height that 215 should be taken up in drawing 216 217 o circular Boolean flaw to show whether the passed sequence is 218 circular or not 219 """ 220 # Use the superclass' instantiation method 221 AbstractDrawer.__init__(self, parent, pagesize, orientation, 222 x, y, xl, xr, yt, yb, start, end, 223 tracklines) 224 225 # Useful measurements on the page 226 self.track_size = track_size 227 if circular == False: # Determine the proportion of the circumference 228 self.sweep = 0.9 # around which information will be drawn 229 else: 230 self.sweep = 1
231 232
233 - def set_track_heights(self):
234 """ set_track_heights(self) 235 236 Since tracks may not be of identical heights, the bottom and top 237 radius for each track is stored in a dictionary - self.track_radii, 238 keyed by track number 239 """ 240 top_track = max(self.drawn_tracks) # The 'highest' track to draw 241 242 trackunit_sum = 0 # Holds total number of 'units' taken up by all tracks 243 trackunits = {} # Holds start and end units for each track keyed by track number 244 heightholder = 0 # placeholder variable 245 for track in range(1, top_track+1): # track numbers to 'draw' 246 try: 247 trackheight = self._parent[track].height # Get track height 248 except: 249 trackheight = 1 # ...or default to 1 250 trackunit_sum += trackheight # increment total track unit height 251 trackunits[track] = (heightholder, heightholder+trackheight) 252 heightholder += trackheight # move to next height 253 trackunit_height = 0.5*min(self.pagewidth, self.pageheight)/trackunit_sum 254 255 # Calculate top and bottom radii for each track 256 self.track_radii = {} # The inner, outer and center radii for each track 257 track_crop = trackunit_height*(1-self.track_size)/2. # 'step back' in pixels 258 for track in trackunits: 259 top = trackunits[track][1]*trackunit_height-track_crop 260 btm = trackunits[track][0]*trackunit_height+track_crop 261 ctr = btm+(top-btm)/2. 262 self.track_radii[track] = (btm, ctr, top)
263
264 - def draw(self):
265 """ draw(self) 266 267 Draw a circular diagram of the stored data 268 """ 269 # Instantiate the drawing canvas 270 self.drawing = Drawing(self.pagesize[0], self.pagesize[1]) 271 272 feature_elements = [] # holds feature elements 273 feature_labels = [] # holds feature labels 274 greytrack_bgs = [] # holds track background 275 greytrack_labels = [] # holds track foreground labels 276 scale_axes = [] # holds scale axes 277 scale_labels = [] # holds scale axis labels 278 279 # Get tracks to be drawn and set track sizes 280 self.drawn_tracks = self._parent.get_drawn_levels() 281 self.set_track_heights() 282 283 # Go through each track in the parent (if it is to be drawn) one by 284 # one and collate the data as drawing elements 285 for track_level in self._parent.get_drawn_levels(): 286 self.current_track_level = track_level 287 track = self._parent[track_level] 288 gbgs, glabels = self.draw_greytrack(track) # Greytracks 289 greytrack_bgs.append(gbgs) 290 greytrack_labels.append(glabels) 291 features, flabels = self.draw_track(track) # Features and graphs 292 feature_elements.append(features) 293 feature_labels.append(flabels) 294 if track.scale: 295 axes, slabels = self.draw_scale(track) # Scale axes 296 scale_axes.append(axes) 297 scale_labels.append(slabels) 298 299 # Groups listed in order of addition to page (from back to front) 300 # Draw track backgrounds 301 # Draw features and graphs 302 # Draw scale axes 303 # Draw scale labels 304 # Draw feature labels 305 # Draw track labels 306 element_groups = [greytrack_bgs, feature_elements, 307 scale_axes, scale_labels, 308 feature_labels, greytrack_labels 309 ] 310 for element_group in element_groups: 311 for element_list in element_group: 312 [self.drawing.add(element) for element in element_list] 313 314 if self.tracklines: # Draw test tracks over top of diagram 315 self.draw_test_tracks()
316 317
318 - def draw_track(self, track):
319 """ draw_track(self, track) -> ([element, element,...], [element, element,...]) 320 321 o track Track object 322 323 Return tuple of (list of track elements, list of track labels) 324 """ 325 track_elements = [] # Holds elements for features and graphs 326 track_labels = [] # Holds labels for features and graphs 327 328 # Distribution dictionary for dealing with different set types 329 set_methods = {FeatureSet: self.draw_feature_set, 330 GraphSet: self.draw_graph_set 331 } 332 333 for set in track.get_sets(): # Draw the feature or graph sets 334 elements, labels = set_methods[set.__class__](set) 335 track_elements += elements 336 track_labels += labels 337 return track_elements, track_labels
338 339
340 - def draw_feature_set(self, set):
341 """ draw_feature_set(self, set) -> ([element, element,...], [element, element,...]) 342 343 o set FeatureSet object 344 345 Returns a tuple (list of elements describing features, list of 346 labels for elements) 347 """ 348 #print 'draw feature set' 349 feature_elements = [] # Holds diagram elements belonging to the features 350 label_elements = [] # Holds diagram elements belonging to feature labels 351 352 # Collect all the elements for the feature set 353 for feature in set.get_features(): 354 if self.is_in_bounds(feature.start) or self.is_in_bounds(feature.end): 355 features, labels = self.draw_feature(feature) 356 feature_elements += features 357 label_elements += labels 358 359 return feature_elements, label_elements
360 361
362 - def draw_feature(self, feature):
363 """ draw_feature(self, feature, parent_feature=None) -> ([element, element,...], [element, element,...]) 364 365 o feature Feature containing location info 366 367 Returns tuple of (list of elements describing single feature, list 368 of labels for those elements) 369 """ 370 feature_elements = [] # Holds drawable elements for a single feature 371 label_elements = [] # Holds labels for a single feature 372 373 if feature.hide: # Don't show feature: return early 374 return feature_elements, label_elements 375 376 # A single feature may be split into subfeatures, so loop over them 377 for locstart, locend in feature.locations: 378 # Get sigil for the feature/ each subfeature 379 feature_sigil, label = self.get_feature_sigil(feature, locstart, locend) 380 feature_elements.append(feature_sigil) 381 if label is not None: # If there's a label 382 label_elements.append(label) 383 384 return feature_elements, label_elements
385 386
387 - def get_feature_sigil(self, feature, locstart, locend):
388 """ get_feature_sigil(self, feature, x0, x1, fragment) -> (element, element) 389 390 o feature Feature object 391 392 o locstart The start position of the feature 393 394 o locend The end position of the feature 395 396 Returns a drawable indicator of the feature, and any required label 397 for it 398 """ 399 # Establish the co-ordinates for the sigil 400 btm, ctr, top = self.track_radii[self.current_track_level] 401 startangle, startcos, startsin = self.canvas_angle(locstart) 402 endangle, endcos, endsin = self.canvas_angle(locend) 403 midangle, midcos, midsin = self.canvas_angle(locend+locstart/2) 404 405 # Distribution dictionary for various ways of drawing the feature 406 # Each method takes the inner and outer radii, the start and end angle 407 # subtended at the diagram center, and the color as arguments 408 draw_methods = {'BOX': self._draw_arc, 409 'ARROW': self._draw_arc_arrow, 410 } 411 412 # Get sigil for the feature, location dependent on the feature strand 413 method = draw_methods[feature.sigil] 414 if feature.color == colors.white: 415 border = colors.black 416 else: 417 border = feature.color 418 if feature.strand == 0: 419 sigil = method(btm, top, startangle, endangle, feature.color, 420 border) 421 if feature.strand == 1: 422 sigil = method(ctr, top, startangle, endangle, feature.color, 423 border, orientation='right') 424 if feature.strand == -1: 425 sigil = method(btm, ctr, startangle, endangle, feature.color, 426 border, orientation='left') 427 if feature.label: # Feature needs a label 428 label = String(0, 0, feature.name.strip(), 429 fontName=feature.label_font, 430 fontSize=feature.label_size, 431 fillColor=feature.label_color) 432 labelgroup = Group(label) 433 label_angle = startangle + 0.5 * pi # Make text radial 434 sinval, cosval = startsin, startcos 435 if feature.strand == 1: # Feature is on top, or covers both strands 436 if startangle < pi: # Turn text round and anchor end to inner radius 437 sinval, cosval = endsin, endcos 438 label_angle = endangle - 0.5 * pi 439 labelgroup.contents[0].textAnchor = 'end' 440 pos = self.xcenter+top*sinval 441 coslabel = cos(label_angle) 442 sinlabel = sin(label_angle) 443 labelgroup.transform = (coslabel,-sinlabel,sinlabel,coslabel, 444 pos, self.ycenter+top*cosval) 445 elif feature.strand == -1: # Feature on bottom strand 446 if startangle > pi: # Anchor end to inner radius 447 labelgroup.contents[0].textAnchor='end' 448 else: # Turn text round 449 sinval, cosval = endsin, endcos 450 label_angle += pi 451 pos = self.xcenter+btm*sinval 452 coslabel = cos(label_angle) 453 sinlabel = sin(label_angle) 454 #labelgroup.transform = (coslabel,-sinlabel,sinlabel,coslabel, 455 # pos, self.ycenter+btm*cosval) 456 labelgroup.transform = (coslabel,-sinlabel,sinlabel,coslabel, 457 pos, self.ycenter+btm*cosval) 458 else: # feature.strand == 0 459 if startangle > pi: # Anchor end to inner radius 460 labelgroup.contents[0].textAnchor='end' 461 sinval, cosval = endsin, endcos 462 else: # Turn text round 463 label_angle += pi 464 pos = self.xcenter+btm*sinval 465 coslabel = cos(label_angle) 466 sinlabel = sin(label_angle) 467 labelgroup.transform = (coslabel,-sinlabel,sinlabel,coslabel, 468 pos, self.ycenter+btm*cosval) 469 else: 470 labelgroup = None 471 #if locstart > locend: 472 # print locstart, locend, feature.strand, sigil, feature.name 473 #print locstart, locend, feature.name 474 return sigil, labelgroup
475 476 477
478 - def draw_graph_set(self, set):
479 """ draw_graph_set(self, set) -> ([element, element,...], [element, element,...]) 480 481 o set GraphSet object 482 483 Returns tuple (list of graph elements, list of graph labels) 484 """ 485 #print 'draw graph set' 486 elements = [] # Holds graph elements 487 488 # Distribution dictionary for how to draw the graph 489 style_methods = {'line': self.draw_line_graph, 490 'heat': self.draw_heat_graph, 491 'bar': self.draw_bar_graph 492 } 493 494 for graph in set.get_graphs(): 495 #print graph.name 496 elements += style_methods[graph.style](graph) 497 498 return elements, []
499 500
501 - def draw_line_graph(self, graph):
502 """ draw_line_graph(self, graph, center) -> [element, element,...] 503 504 o graph GraphData object 505 506 Returns a line graph as a list of drawable elements 507 """ 508 #print '\tdraw_line_graph' 509 line_elements = [] # holds drawable elements 510 511 # Get graph data 512 data_quartiles = graph.quartiles() 513 minval, maxval = data_quartiles[0],data_quartiles[4] 514 btm, ctr, top = self.track_radii[self.current_track_level] 515 trackheight = 0.5*(top-btm) 516 datarange = maxval - minval 517 if datarange == 0: 518 datarange = trackheight 519 data = graph[self.start:self.end] 520 521 # midval is the value at which the x-axis is plotted, and is the 522 # central ring in the track 523 if graph.center is None: 524 midval = (maxval + minval)/2. 525 else: 526 midval = graph.center 527 # Whichever is the greatest difference: max-midval or min-midval, is 528 # taken to specify the number of pixel units resolved along the 529 # y-axis 530 resolution = max((midval-minval), (maxval-midval)) 531 532 # Start from first data point 533 pos, val = data[0] 534 lastangle, lastcos, lastsin = self.canvas_angle(pos) 535 # We calculate the track height 536 posheight = trackheight*(val-midval)/resolution + ctr 537 lastx = self.xcenter+posheight*lastsin # start xy coords 538 lasty = self.ycenter+posheight*lastcos 539 for pos, val in data: 540 posangle, poscos, possin = self.canvas_angle(pos) 541 posheight = trackheight*(val-midval)/resolution + ctr 542 x = self.xcenter+posheight*possin # next xy coords 543 y = self.ycenter+posheight*poscos 544 line_elements.append(Line(lastx, lasty, x, y, 545 strokeColor = graph.poscolor, 546 strokeWidth = graph.linewidth)) 547 lastx, lasty, = x, y 548 return line_elements
549 550
551 - def draw_bar_graph(self, graph):
552 """ draw_bar_graph(self, graph) -> [element, element,...] 553 554 o graph Graph object 555 556 Returns a list of drawable elements for a bar graph of the passed 557 Graph object 558 """ 559 #print '\tdraw_bar_graph' 560 # At each point contained in the graph data, we draw a vertical bar 561 # from the track center to the height of the datapoint value (positive 562 # values go up in one color, negative go down in the alternative 563 # color). 564 bar_elements = [] 565 566 # Set the number of pixels per unit for the data 567 data_quartiles = graph.quartiles() 568 minval, maxval = data_quartiles[0],data_quartiles[4] 569 btm, ctr, top = self.track_radii[self.current_track_level] 570 trackheight = 0.5*(top-btm) 571 datarange = maxval - minval 572 if datarange == 0: 573 datarange = trackheight 574 data = graph[self.start:self.end] 575 # midval is the value at which the x-axis is plotted, and is the 576 # central ring in the track 577 if graph.center is None: 578 midval = (maxval + minval)/2. 579 else: 580 midval = graph.center 581 582 # Convert data into 'binned' blocks, covering half the distance to the 583 # next data point on either side, accounting for the ends of fragments 584 # and tracks 585 newdata = intermediate_points(self.start, self.end, 586 graph[self.start:self.end]) 587 588 # Whichever is the greatest difference: max-midval or min-midval, is 589 # taken to specify the number of pixel units resolved along the 590 # y-axis 591 resolution = max((midval-minval), (maxval-midval)) 592 if resolution == 0: 593 resolution = trackheight 594 595 # Create elements for the bar graph based on newdata 596 for pos0, pos1, val in newdata: 597 pos0angle, pos0cos, pos0sin = self.canvas_angle(pos0) 598 pos1angle, pos1cos, pos1sin = self.canvas_angle(pos1) 599 600 barval = trackheight*(val-midval)/resolution 601 if barval >=0: 602 barcolor = graph.poscolor 603 else: 604 barcolor = graph.negcolor 605 606 # Draw bar 607 bar_elements.append(self._draw_arc(ctr, ctr+barval, pos0angle, 608 pos1angle, barcolor)) 609 return bar_elements
610 611 612 613
614 - def draw_heat_graph(self, graph):
615 """ draw_heat_graph(self, graph) -> [element, element,...] 616 617 o graph Graph object 618 619 Returns a list of drawable elements for the heat graph 620 """ 621 #print '\tdraw_heat_graph' 622 # At each point contained in the graph data, we draw a box that is the 623 # full height of the track, extending from the midpoint between the 624 # previous and current data points to the midpoint between the current 625 # and next data points 626 heat_elements = [] # holds drawable elements 627 628 # Get graph data 629 data_quartiles = graph.quartiles() 630 minval, maxval = data_quartiles[0],data_quartiles[4] 631 midval = (maxval + minval)/2. # mid is the value at the X-axis 632 btm, ctr, top = self.track_radii[self.current_track_level] 633 trackheight = (top-btm) 634 newdata = intermediate_points(self.start, self.end, 635 graph[self.start:self.end]) 636 637 # Create elements on the graph, indicating a large positive value by 638 # the graph's poscolor, and a large negative value by the graph's 639 # negcolor attributes 640 for pos0, pos1, val in newdata: 641 pos0angle, pos0cos, pos0sin = self.canvas_angle(pos0) 642 pos1angle, pos1cos, pos1sin = self.canvas_angle(pos1) 643 644 # Calculate the heat color, based on the differential between 645 # the value and the median value 646 heat = colors.linearlyInterpolatedColor(graph.poscolor, 647 graph.negcolor, 648 maxval, minval, val) 649 650 # Draw heat box 651 heat_elements.append(self._draw_arc(btm, top, pos0angle, pos1angle, 652 heat, border=heat)) 653 return heat_elements
654 655
656 - def draw_scale(self, track):
657 """ draw_scale(self, track) -> ([element, element,...], [element, element,...]) 658 659 o track Track object 660 661 Returns a tuple of (list of elements in the scale, list of labels 662 in the scale) 663 """ 664 scale_elements = [] # holds axes and ticks 665 scale_labels = [] # holds labels 666 667 if not track.scale: # no scale required, exit early 668 return [], [] 669 670 # Get track locations 671 btm, ctr, top = self.track_radii[self.current_track_level] 672 trackheight = (top-ctr) 673 674 # X-axis 675 if self.sweep < 1 : 676 #Draw an arc, leaving out the wedge 677 p = ArcPath(strokeColor=track.scale_color, fillColor=None) 678 #Note reportlab counts angles anti-clockwise from the horizontal 679 #(as in mathematics, e.g. complex numbers and polar coordinates) 680 #in degrees. 681 p.addArc(self.xcenter, self.ycenter, ctr, 682 startangledegrees=90-360*self.sweep, 683 endangledegrees=90) 684 scale_elements.append(p) 685 del p 686 else : 687 #Draw a full circle 688 scale_elements.append(Circle(self.xcenter, self.ycenter, ctr, 689 strokeColor=track.scale_color, 690 fillColor=None)) 691 692 if track.scale_ticks: # Ticks are required on the scale 693 # Draw large ticks 694 #I want the ticks to be consistently positioned relative to 695 #the start of the sequence (position 0), not relative to the 696 #current viewpoint (self.start and self.end) 697 698 ticklen = track.scale_largeticks * trackheight 699 tickiterval = int(track.scale_largetick_interval) 700 #Note that we could just start the list of ticks using 701 #range(0,self.end,tickinterval) and the filter out the 702 #ones before self.start - but this seems wasteful. 703 #Using tickiterval * (self.start/tickiterval) is a shortcut. 704 largeticks = [pos for pos \ 705 in range(tickiterval * (self.start/tickiterval), 706 int(self.end), 707 tickiterval) \ 708 if pos >= self.start] 709 for tickpos in largeticks: 710 tick, label = self.draw_tick(tickpos, ctr, ticklen, 711 track, 712 track.scale_largetick_labels) 713 scale_elements.append(tick) 714 if label is not None: # If there's a label, add it 715 scale_labels.append(label) 716 # Draw small ticks 717 ticklen = track.scale_smallticks * trackheight 718 tickiterval = int(track.scale_smalltick_interval) 719 smallticks = [pos for pos \ 720 in range(tickiterval * (self.start/tickiterval), 721 int(self.end), 722 tickiterval) \ 723 if pos >= self.start] 724 for tickpos in smallticks: 725 tick, label = self.draw_tick(tickpos, ctr, ticklen, 726 track, 727 track.scale_smalltick_labels) 728 scale_elements.append(tick) 729 if label is not None: # If there's a label, add it 730 scale_labels.append(label) 731 732 # Check to see if the track contains a graph - if it does, get the 733 # minimum and maximum values, and put them on the scale Y-axis 734 # at 60 degree intervals, ordering the labels by graph_id 735 if track.axis_labels: 736 for set in track.get_sets(): 737 if set.__class__ is GraphSet: 738 # Y-axis 739 for n in xrange(7): 740 angle = n * 1.0471975511965976 741 ticksin, tickcos = sin(angle), cos(angle) 742 x0, y0 = self.xcenter+btm*ticksin, self.ycenter+btm*tickcos 743 x1, y1 = self.xcenter+top*ticksin, self.ycenter+top*tickcos 744 scale_elements.append(Line(x0, y0, x1, y1, 745 strokeColor=track.scale_color)) 746 747 graph_label_min = [] 748 graph_label_max = [] 749 graph_label_mid = [] 750 for graph in set.get_graphs(): 751 quartiles = graph.quartiles() 752 minval, maxval = quartiles[0], quartiles[4] 753 if graph.center is None: 754 midval = (maxval + minval)/2. 755 graph_label_min.append("%.3f" % minval) 756 graph_label_max.append("%.3f" % maxval) 757 graph_label_mid.append("%.3f" % midval) 758 else: 759 diff = max((graph.center-minval), 760 (maxval-graph.center)) 761 minval = graph.center-diff 762 maxval = graph.center+diff 763 midval = graph.center 764 graph_label_mid.append("%.3f" % midval) 765 graph_label_min.append("%.3f" % minval) 766 graph_label_max.append("%.3f" % maxval) 767 xmid, ymid = (x0+x1)/2., (y0+y1)/2. 768 for limit, x, y, in [(graph_label_min, x0, y0), 769 (graph_label_max, x1, y1), 770 (graph_label_mid, xmid, ymid)]: 771 label = String(0, 0, ";".join(limit), 772 fontName=track.scale_font, 773 fontSize=track.scale_fontsize, 774 fillColor=track.scale_color) 775 label.textAnchor = 'middle' 776 labelgroup = Group(label) 777 labelgroup.transform = (tickcos, -ticksin, 778 ticksin, tickcos, 779 x, y) 780 scale_labels.append(labelgroup) 781 782 return scale_elements, scale_labels
783 784
785 - def draw_tick(self, tickpos, ctr, ticklen, track, draw_label):
786 """ draw_tick(self, tickpos, ctr, ticklen) -> (element, element) 787 788 o tickpos Int, position of the tick on the sequence 789 790 o ctr Float, Y co-ord of the center of the track 791 792 o ticklen How long to draw the tick 793 794 o track Track, the track the tick is drawn on 795 796 o draw_label Boolean, write the tick label? 797 798 Returns a drawing element that is the tick on the scale 799 """ 800 # Calculate tick co-ordinates 801 tickangle, tickcos, ticksin = self.canvas_angle(tickpos) 802 x0, y0 = self.xcenter+ctr*ticksin, self.ycenter+ctr*tickcos 803 x1, y1 = self.xcenter+(ctr+ticklen)*ticksin, self.ycenter+(ctr+ticklen)*tickcos 804 # Calculate height of text label so it can be offset on lower half 805 # of diagram 806 # LP: not used, as not all fonts have ascent_descent data in reportlab.pdfbase._fontdata 807 #label_offset = _fontdata.ascent_descent[track.scale_font][0]*\ 808 # track.scale_fontsize/1000. 809 tick = Line(x0, y0, x1, y1, strokeColor=track.scale_color) 810 if draw_label: # Put tick position on as label 811 if track.scale_format == 'SInt': 812 if tickpos >= 1000000: 813 tickstring = str(tickpos/1000000) + " Mbp" 814 elif tickpos >= 1000: 815 tickstring = str(tickpos/1000) + " Kbp" 816 else: 817 tickstring = str(tickpos) 818 else: 819 tickstring = str(tickpos) 820 label = String(0, 0, tickstring, # Make label string 821 fontName=track.scale_font, 822 fontSize=track.scale_fontsize, 823 fillColor=track.scale_color) 824 if tickangle > pi: 825 label.textAnchor = 'end' 826 # LP: This label_offset depends on ascent_descent data, which is not available for all 827 # fonts, so has been deprecated. 828 #if 0.5*pi < tickangle < 1.5*pi: 829 # y1 -= label_offset 830 labelgroup = Group(label) 831 labelgroup.transform = (1,0,0,1, x1, y1) 832 else: 833 labelgroup = None 834 return tick, labelgroup
835 836
837 - def draw_test_tracks(self):
838 """ draw_test_tracks(self) 839 840 Draw blue ones indicating tracks to be drawn, with a green line 841 down the center. 842 """ 843 #print 'drawing test tracks' 844 # Add lines only for drawn tracks 845 for track in self.drawn_tracks: 846 btm, ctr, top = self.track_radii[track] 847 self.drawing.add(Circle(self.xcenter, self.ycenter, top, 848 strokeColor=colors.blue, 849 fillColor=None)) # top line 850 self.drawing.add(Circle(self.xcenter, self.ycenter, ctr, 851 strokeColor=colors.green, 852 fillColor=None)) # middle line 853 self.drawing.add(Circle(self.xcenter, self.ycenter, btm, 854 strokeColor=colors.blue, 855 fillColor=None)) # bottom line
856 857
858 - def draw_greytrack(self, track):
859 """ draw_greytrack(self) 860 861 o track Track object 862 863 Put in a grey background to the current track, if the track 864 specifies that we should 865 """ 866 greytrack_bgs = [] # Holds track backgrounds 867 greytrack_labels = [] # Holds track foreground labels 868 869 if not track.greytrack: # No greytrack required, return early 870 return [], [] 871 872 # Get track location 873 btm, ctr, top = self.track_radii[self.current_track_level] 874 875 # Make background 876 if self.sweep < 1 : 877 #Make a partial circle, a large arc box 878 #This method assumes the correct center for us. 879 bg = self._draw_arc(btm, top, 0, 2*pi*self.sweep, 880 colors.Color(0.98, 0.98, 0.98)) 881 else : 882 #Make a full circle (using a VERY thick linewidth) 883 bg = Circle(self.xcenter, self.ycenter, ctr, 884 strokeColor = colors.Color(0.98, 0.98, 0.98), 885 fillColor=None, strokeWidth=top-btm) 886 greytrack_bgs.append(bg) 887 888 if track.greytrack_labels: # Labels are required for this track 889 labelstep = self.length/track.greytrack_labels # label interval 890 for pos in range(self.start, self.end, int(labelstep)): 891 label = String(0, 0, track.name, # Add a new label at 892 fontName=track.greytrack_font, # each interval 893 fontSize=track.greytrack_fontsize, 894 fillColor=track.greytrack_fontcolor) 895 theta, costheta, sintheta = self.canvas_angle(pos) 896 x,y = self.xcenter+btm*sintheta, self.ycenter+btm*costheta # start text halfway up marker 897 labelgroup = Group(label) 898 labelangle = self.sweep*2*pi*(pos-self.start)/self.length - pi/2 899 if theta > pi: 900 label.textAnchor = 'end' # Anchor end of text to inner radius 901 labelangle += pi # and reorient it 902 cosA, sinA = cos(labelangle), sin(labelangle) 903 labelgroup.transform = (cosA, -sinA, sinA, 904 cosA, x, y) 905 if not self.length-x <= labelstep: # Don't overrun the circle 906 greytrack_labels.append(labelgroup) 907 908 return greytrack_bgs, greytrack_labels
909 910
911 - def canvas_angle(self, base):
912 """ canvas_angle(self, base) -> (float, float, float) 913 """ 914 angle = self.sweep*2*pi*(base-self.start)/self.length 915 return (angle, cos(angle), sin(angle))
916 917
918 - def _draw_arc(self, inner_radius, outer_radius, startangle, endangle, 919 color, border=None, colour=None, **kwargs):
920 """ draw_arc(self, inner_radius, outer_radius, startangle, endangle, color) 921 -> Group 922 923 o inner_radius Float distance of inside of arc from drawing center 924 925 o outer_radius Float distance of outside of arc from drawing center 926 927 o startangle Float angle subtended by start of arc at drawing center 928 (in radians) 929 930 o endangle Float angle subtended by end of arc at drawing center 931 (in radians) 932 933 o color colors.Color object for arc (overridden by backwards 934 compatible argument with UK spelling, colour). 935 936 Returns a closed path object describing an arced box corresponding to 937 the passed values. For very small angles, a simple four sided 938 polygon is used. 939 """ 940 #Let the UK spelling (colour) override the USA spelling (color) 941 if colour is not None: 942 color = colour 943 944 if border is None: 945 border = color 946 947 if color is None: 948 color = colour 949 if color == colors.white and border is None: # Force black border on 950 strokecolor = colors.black # white boxes with 951 elif border is None: # undefined border, else 952 strokecolor = color # use fill colour 953 elif border is not None: 954 strokecolor = border 955 956 angle = float(endangle - startangle) # angle subtended by arc 957 if angle>.01: # Wide arc, represent with multiple boxes 958 p = ArcPath(strokeColor=strokecolor, 959 fillColor=color, 960 strokewidth=0) 961 #Note reportlab counts angles anti-clockwise from the horizontal 962 #(as in mathematics, e.g. complex numbers and polar coordinates) 963 #but we use clockwise from the vertical. Also reportlab uses 964 #degrees, but we use radians. 965 p.addArc(self.xcenter, self.ycenter, inner_radius, 966 90 - (endangle * 180 / pi), 90 - (startangle * 180 / pi), 967 moveTo=True) 968 p.addArc(self.xcenter, self.ycenter, outer_radius, 969 90 - (endangle * 180 / pi), 90 - (startangle * 180 / pi), 970 reverse=True) 971 p.closePath() 972 return p 973 else : 974 #Cheat and just use a four sided polygon. 975 # Calculate trig values for angle and coordinates 976 startcos, startsin = cos(startangle), sin(startangle) 977 endcos, endsin = cos(endangle), sin(endangle) 978 x0,y0 = self.xcenter, self.ycenter # origin of the circle 979 x1,y1 = (x0+inner_radius*startsin, y0+inner_radius*startcos) 980 x2,y2 = (x0+inner_radius*endsin, y0+inner_radius*endcos) 981 x3,y3 = (x0+outer_radius*endsin, y0+outer_radius*endcos) 982 x4,y4 = (x0+outer_radius*startsin, y0+outer_radius*startcos) 983 return draw_polygon([(x1,y1),(x2,y2),(x3,y3),(x4,y4)], color, border)
984
985 - def _draw_arc_arrow(self, inner_radius, outer_radius, startangle, endangle, 986 color, border=None, 987 shaft_height_ratio=0.4, head_length_ratio=0.5, orientation='right', 988 colour=None, **kwargs):
989 """Draw an arrow along an arc.""" 990 #Let the UK spelling (colour) override the USA spelling (color) 991 if colour is not None: 992 color = colour 993 994 if border is None: 995 border = color 996 997 if color is None: 998 color = colour 999 if color == colors.white and border is None: # Force black border on 1000 strokecolor = colors.black # white boxes with 1001 elif border is None: # undefined border, else 1002 strokecolor = color # use fill colour 1003 elif border is not None: 1004 strokecolor = border 1005 1006 #if orientation == 'right': 1007 # startangle, endangle = min(startangle, endangle), max(startangle, endangle) 1008 #elif orientation == 'left': 1009 # startangle, endangle = max(startangle, endangle), min(startangle, endangle) 1010 #else : 1011 startangle, endangle = min(startangle, endangle), max(startangle, endangle) 1012 if orientation <> "left" and orientation <> "right" : 1013 raise ValueError("Invalid orientation %s, should be 'left' or 'right'" \ 1014 % repr(orientation)) 1015 1016 angle = float(endangle - startangle) # angle subtended by arc 1017 middle_radius = 0.5*(inner_radius+outer_radius) 1018 boxheight = outer_radius - inner_radius 1019 shaft_height = boxheight*shaft_height_ratio 1020 shaft_inner_radius = middle_radius - 0.5*shaft_height 1021 shaft_outer_radius = middle_radius + 0.5*shaft_height 1022 headangle_delta = min(abs(asin(boxheight/middle_radius)*head_length_ratio), abs(angle)) 1023 if angle < 0 : 1024 headangle_delta *= -1 #reverse it 1025 if orientation=="right" : 1026 headangle = endangle-headangle_delta 1027 else : 1028 headangle = startangle+headangle_delta 1029 if startangle <= endangle : 1030 headangle = max(min(headangle, endangle), startangle) 1031 else : 1032 headangle = max(min(headangle, startangle), endangle) 1033 assert startangle <= headangle <= endangle \ 1034 or endangle <= headangle <= startangle 1035 1036 1037 # Calculate trig values for angle and coordinates 1038 startcos, startsin = cos(startangle), sin(startangle) 1039 headcos, headsin = cos(headangle), sin(headangle) 1040 endcos, endsin = cos(endangle), sin(endangle) 1041 x0,y0 = self.xcenter, self.ycenter # origin of the circle 1042 if abs(headangle_delta) >= abs(angle) : 1043 #Cheat and just use a triangle. 1044 if orientation=="right" : 1045 x1,y1 = (x0+inner_radius*startsin, y0+inner_radius*startcos) 1046 x2,y2 = (x0+outer_radius*startsin, y0+outer_radius*startcos) 1047 x3,y3 = (x0+middle_radius*endsin, y0+middle_radius*endcos) 1048 else : 1049 x1,y1 = (x0+inner_radius*endsin, y0+inner_radius*endcos) 1050 x2,y2 = (x0+outer_radius*endsin, y0+outer_radius*endcos) 1051 x3,y3 = (x0+middle_radius*startsin, y0+middle_radius*startcos) 1052 return draw_polygon([(x1,y1),(x2,y2),(x3,y3)], color, border) 1053 elif orientation=="right" : 1054 p = ArcPath(strokeColor=strokecolor, 1055 fillColor=color, 1056 #default is mitre/miter which can stick out too much: 1057 strokeLineJoin=1, #1=round 1058 strokewidth=0) 1059 #Note reportlab counts angles anti-clockwise from the horizontal 1060 #(as in mathematics, e.g. complex numbers and polar coordinates) 1061 #but we use clockwise from the vertical. Also reportlab uses 1062 #degrees, but we use radians. 1063 p.addArc(self.xcenter, self.ycenter, shaft_inner_radius, 1064 90 - (headangle * 180 / pi), 90 - (startangle * 180 / pi), 1065 moveTo=True) 1066 p.addArc(self.xcenter, self.ycenter, shaft_outer_radius, 1067 90 - (headangle * 180 / pi), 90 - (startangle * 180 / pi), 1068 reverse=True) 1069 p.lineTo(x0+outer_radius*headsin, y0+outer_radius*headcos) 1070 p.lineTo(x0+middle_radius*endsin, y0+middle_radius*endcos) 1071 p.lineTo(x0+inner_radius*headsin, y0+inner_radius*headcos) 1072 p.closePath() 1073 return p 1074 else : 1075 p = ArcPath(strokeColor=strokecolor, 1076 fillColor=color, 1077 #default is mitre/miter which can stick out too much: 1078 strokeLineJoin=1, #1=round 1079 strokewidth=0) 1080 #Note reportlab counts angles anti-clockwise from the horizontal 1081 #(as in mathematics, e.g. complex numbers and polar coordinates) 1082 #but we use clockwise from the vertical. Also reportlab uses 1083 #degrees, but we use radians. 1084 p.addArc(self.xcenter, self.ycenter, shaft_inner_radius, 1085 90 - (endangle * 180 / pi), 90 - (headangle * 180 / pi), 1086 moveTo=True, reverse=True) 1087 p.addArc(self.xcenter, self.ycenter, shaft_outer_radius, 1088 90 - (endangle * 180 / pi), 90 - (headangle * 180 / pi), 1089 reverse=False) 1090 p.lineTo(x0+outer_radius*headsin, y0+outer_radius*headcos) 1091 p.lineTo(x0+middle_radius*startsin, y0+middle_radius*startcos) 1092 p.lineTo(x0+inner_radius*headsin, y0+inner_radius*headcos) 1093 p.closePath() 1094 return p
1095