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# 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
# [email protected]
################################################################################
"""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.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.strand,
color=feature.color,
border=feature.border,
**kwargs,
)
if feature.label_strand:
strand = feature.label_strand
else:
strand = feature.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)
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