def writeGrid(self):
"""add grid lines."""
min_x = self.mHeaderWidth
max_x = min_x + self.mDataWidth
min_y = self.mHeaderHeight
max_y = min_y + self.mDataHeight
for contig in self.mSortedContigs1:
if contig not in self.mMapContig2Start1:
continue
x = self.mMapContig2Start1[contig]
e = SVGdraw.line(min_x + x, min_y, min_x + x, max_y,
stroke="rgb(%i,%i,%i)" % GREEN,
)
self.addElement(e)
self.addElement(SVGdraw.line(max_x, min_y, max_x, max_y,
stroke="rgb(%i,%i,%i)" % GREEN))
for contig in self.mSortedContigs2:
if contig not in self.mMapContig2Start2:
continue
y = self.mMapContig2Start2[contig]
e = SVGdraw.line(min_x, min_y + y, max_x, min_y + y,
stroke="rgb(%i,%i,%i)" % GREEN,
)
self.addElement(e)
self.addElement(SVGdraw.line(min_x, max_y, max_x, max_y,
stroke="rgb(%i,%i,%i)" % GREEN))
def writeGrid(self):
"""add grid lines."""
min_x = self.mHeaderWidth
max_x = min_x + self.mDataWidth
min_y = self.mHeaderHeight
max_y = min_y + self.mDataHeight
for contig in self.mSortedContigs1:
if contig not in self.mMapContig2Start1:
continue
x = self.mMapContig2Start1[contig]
e = SVGdraw.line(
min_x + x,
min_y,
min_x + x,
max_y,
stroke="rgb(%i,%i,%i)" % GREEN,
)
self.addElement(e)
self.addElement(
SVGdraw.line(max_x,
min_y,
max_x,
max_y,
stroke="rgb(%i,%i,%i)" % GREEN))
for contig in self.mSortedContigs2:
if contig not in self.mMapContig2Start2:
continue
y = self.mMapContig2Start2[contig]
e = SVGdraw.line(
min_x,
min_y + y,
max_x,
min_y + y,
stroke="rgb(%i,%i,%i)" % GREEN,
)
self.addElement(e)
self.addElement(
SVGdraw.line(min_x,
max_y,
max_x,
max_y,
stroke="rgb(%i,%i,%i)" % GREEN))
def getElements(self, node_id, x, y1, y2):
e = []
e.append(SVGdraw.line(x, y1, x, y2,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1))
return e
def addGroupStart(self, x, y, contig, start):
"""plot start of contig."""
t = "%s:%i" % (contig, start)
max_x = x + len(t) * self.contigFontSize * self.mFontFactor
## plot line
e = SVGdraw.line(
x,
y,
max_x,
y,
stroke="rgb(%i,%i,%i)" % BLACK,
)
self.addElement(e)
e = SVGdraw.text(x,
y,
t,
self.contigFontSize,
self.contigFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="left")
self.addElement(e)
return max_x
def getElements(self, node_id, x1, x2, y):
e = []
if not self.mNoBranch:
e.append(SVGdraw.line(x1, y, x2, y,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1))
return e
def writeFooter(self):
"""write footer.
The footer contains the legend.
"""
current_x = self.mFooterFrom
current_y = self.mHeaderHeight + self.mDataHeight + 2 * self.mSeparator
self.mFooterBoxSize = 30
self.mNumTicks = 20
for x in range(len(self.mColourThresholds)):
e = SVGdraw.rect(current_x,
current_y,
self.mFooterBoxSize,
self.mFooterBoxSize,
fill="rgb(%i,%i,%i)" % self.mColours[x],
stroke="rgb(%i,%i,%i)" % self.mColours[x])
self.addElement(e)
if x % self.mNumTicks == 0:
e = SVGdraw.line(current_x,
current_y,
current_x,
current_y + self.mFooterBoxSize,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=5)
self.addElement(e)
e = SVGdraw.text(current_x,
current_y - self.mFooterBoxSize,
self.mFormatNumberLegend %
self.mColourThresholds[x],
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
self.addElement(e)
current_x += self.mFooterBoxSize
###########################################################
if self.mFooter:
current_y += max(self.mFooterFontSize,
self.mMaxBoxSize) + self.mSeparator
e = SVGdraw.text(self.mPageWidth / 2,
current_y + self.mFooterFontSize,
self.mFooter,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
self.addElement(e)
def writeFooter(self):
"""write footer.
The footer contains the legend.
"""
current_x = self.mFooterFrom
current_y = self.mHeaderHeight + self.mDataHeight + 2 * self.mSeparator
self.mFooterBoxSize = 30
self.mNumTicks = 20
for x in range(len(self.mColourThresholds)):
e = SVGdraw.rect(current_x,
current_y,
self.mFooterBoxSize,
self.mFooterBoxSize,
fill="rgb(%i,%i,%i)" % self.mColours[x],
stroke="rgb(%i,%i,%i)" % self.mColours[x])
self.addElement(e)
if x % self.mNumTicks == 0:
e = SVGdraw.line(current_x,
current_y,
current_x,
current_y + self.mFooterBoxSize,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=5)
self.addElement(e)
e = SVGdraw.text(current_x,
current_y - self.mFooterBoxSize,
self.mFormatNumberLegend % self.mColourThresholds[
x],
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
self.addElement(e)
current_x += self.mFooterBoxSize
###########################################################
if self.mFooter:
current_y += max(self.mFooterFontSize,
self.mMaxBoxSize) + self.mSeparator
e = SVGdraw.text(self.mPageWidth / 2,
current_y + self.mFooterFontSize,
self.mFooter,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
self.addElement(e)
def writeGrid(self):
"""add grid lines."""
if self.mRowTicks:
start_x = 0,
end_x = self.mDataWidth + self.mSeparator + self.mHeaderWidth
current_y = self.mHeaderHeight + self.mSeparator / \
2 + self.mRowTicks * self.mRowHeight
for x in range(self.mRowTicks, len(self.mRowNames),
self.mRowTicks):
e = SVGdraw.line(start_x,
current_y,
end_x,
current_y,
stroke="rgb(%i,%i,%i)" % BLACK)
self.mElements.append(e)
current_y += self.mRowTicks * self.mRowHeight
if self.mColTicks:
start_y = self.mHeaderHeight + self.mSeparator / 2
end_y = start_y + self.mDataHeight
current_x = self.mColTicks * self.mColWidth - self.mColWidth / 2
for x in range(self.mColTicks, len(self.mColNames),
self.mColTicks):
e = SVGdraw.line(current_x,
start_y,
current_x,
end_y,
stroke="rgb(%i,%i,%i)" % BLACK)
self.mElements.append(e)
current_x += self.mColTicks * self.mColWidth
def writeGrid(self):
"""add grid lines."""
if self.mRowTicks:
start_x = 0,
end_x = self.mDataWidth + self.mSeparator + self.mHeaderWidth
current_y = self.mHeaderHeight + self.mSeparator / \
2 + self.mRowTicks * self.mRowHeight
for x in range(self.mRowTicks, len(self.mRowNames),
self.mRowTicks):
e = SVGdraw.line(start_x,
current_y,
end_x,
current_y,
stroke="rgb(%i,%i,%i)" % BLACK)
self.mElements.append(e)
current_y += self.mRowTicks * self.mRowHeight
if self.mColTicks:
start_y = self.mHeaderHeight + self.mSeparator / 2
end_y = start_y + self.mDataHeight
current_x = self.mColTicks * self.mColWidth - self.mColWidth / 2
for x in range(self.mColTicks, len(self.mColNames),
self.mColTicks):
e = SVGdraw.line(current_x,
start_y,
current_x,
end_y,
stroke="rgb(%i,%i,%i)" % BLACK)
self.mElements.append(e)
current_x += self.mColTicks * self.mColWidth
def getElements(self, node_id, x1, x2, y):
e = []
e.append(SVGdraw.line(x1, y, x2, y,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1))
e += self.mDecorator1.getElements(node_id, x1, x2, y)
e += self.mDecorator2.getElements(node_id, x1, x2, y + self.mFontSize)
return e
def getElements(self, node_id, x, y1, y2):
e = []
e.append(
SVGdraw.line(x,
y1,
x,
y2,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1))
return e
def getElements(self, node_id, x1, x2, y):
e = []
if not self.mNoBranch:
e.append(
SVGdraw.line(x1,
y,
x2,
y,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1))
return e
def writeScale(self):
"""write scales."""
current_x = self.mScaleX
current_y = self.mScaleY + self.mScaleHeight
nboxes = len(self.mColourThresholds)
# box size for legend in x-direction
# subtract size of right-most axis label so that it takes the
# same width as self.mDataWidth.
box_size_x = math.ceil((self.mDataWidth -
(self.mScaleFontSize * len(
self.mFormatNumberLegend %
self.mColourThresholds[-1]))) / nboxes)
# change font size such that it labels will fit between tick-marks
self.mScaleFontSize = min(self.mScaleFontSize,
(box_size_x * self.mScaleNumTicks * 1.5) /
len(self.mFormatNumberLegend %
self.mColourThresholds[-1]))
for x in range(nboxes):
e = SVGdraw.rect(current_x,
current_y,
box_size_x,
self.mScaleBoxSizeY,
fill="rgb(%i,%i,%i)" % self.mColours[x],
stroke="rgb(%i,%i,%i)" % self.mColours[x])
self.addElement(e)
if x % self.mScaleNumTicks == 0:
e = SVGdraw.line(current_x,
current_y,
current_x,
current_y + self.mScaleBoxSizeY,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=5)
self.addElement(e)
e = SVGdraw.text(current_x,
current_y - self.mScaleBoxSizeY,
self.mFormatNumberLegend % self.mColourThresholds[
x],
self.mScaleFontSize,
self.mScaleFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
self.addElement(e)
current_x += box_size_x
def writeScale(self):
"""write scales."""
current_x = self.mScaleX
current_y = self.mScaleY + self.mScaleHeight
nboxes = len(self.mColourThresholds)
# box size for legend in x-direction
# subtract size of right-most axis label so that it takes the
# same width as self.mDataWidth.
box_size_x = math.ceil(
(self.mDataWidth -
(self.mScaleFontSize *
len(self.mFormatNumberLegend % self.mColourThresholds[-1]))) /
nboxes)
# change font size such that it labels will fit between tick-marks
self.mScaleFontSize = min(
self.mScaleFontSize, (box_size_x * self.mScaleNumTicks * 1.5) /
len(self.mFormatNumberLegend % self.mColourThresholds[-1]))
for x in range(nboxes):
e = SVGdraw.rect(current_x,
current_y,
box_size_x,
self.mScaleBoxSizeY,
fill="rgb(%i,%i,%i)" % self.mColours[x],
stroke="rgb(%i,%i,%i)" % self.mColours[x])
self.addElement(e)
if x % self.mScaleNumTicks == 0:
e = SVGdraw.line(current_x,
current_y,
current_x,
current_y + self.mScaleBoxSizeY,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=5)
self.addElement(e)
e = SVGdraw.text(current_x,
current_y - self.mScaleBoxSizeY,
self.mFormatNumberLegend %
self.mColourThresholds[x],
self.mScaleFontSize,
self.mScaleFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
self.addElement(e)
current_x += box_size_x
def getElements(self, node_id, x1, x2, y):
e = []
e.append(
SVGdraw.line(x1,
y,
x2,
y,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1))
e += self.mDecorator1.getElements(node_id, x1, x2, y)
e += self.mDecorator2.getElements(node_id, x1, x2, y + self.mFontSize)
return e
def plotLinksForPair(self, species1, species2, colour=BLACK, plane=0):
"""plot links."""
if species1 not in self.mOrthologs or species2 not in self.mOrthologs:
return
for group1 in self.mOrthologs[species1]:
if group1 in self.mOrthologs[species2]:
for g1 in self.mOrthologs[species1][group1]:
for g2 in self.mOrthologs[species2][group1]:
x1, y1 = self.mMapGene2Coord[g1]
x2, y2 = self.mMapGene2Coord[g2]
e = SVGdraw.line(x1, y1, x2, y2, stroke="rgb(%i,%i,%i)" % colour)
self.addElement(e, plane=plane)
def addGroupStart(self, x, y, contig, start):
"""plot start of contig."""
t = "%s:%i" % (contig, start)
max_x = x + len(t) * self.contigFontSize * self.mFontFactor
# plot line
e = SVGdraw.line(x, y, max_x, y, stroke="rgb(%i,%i,%i)" % BLACK)
self.addElement(e)
e = SVGdraw.text(
x, y, t, self.contigFontSize, self.contigFont, stroke="rgb(%i,%i,%i)" % BLACK, text_anchor="left"
)
self.addElement(e)
return max_x
def writeGrid(self):
"""add grid lines."""
middlex = self.mDataMiddleX
middley = self.mDataMiddleY
# print separators
for c in range(len(self.contigs)):
contig = self.contigs[c]
pos = self.getPosition(contig, "+", 0)
angle = self.getAngle(pos)
x, y = self.getPosOnArc(angle, self.mRadius)
e = SVGdraw.line(middlex,
middley,
x,
y,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=self.mGridStrokeWidth)
self.addElement(e, self.mPlaneGrid)
if c < len(self.contigs) - 1:
next_angle = self.getAngle(
self.getPosition(self.contigs[c + 1], "+", 0))
else:
next_angle = 360
x, y = self.getPosOnArc(
angle + float(next_angle - angle) / 2, self.mRadiusStart / 2)
e = SVGdraw.text(x,
y,
contig,
self.mGridFontSize,
self.mGridFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
# do not rotate text:
# transform="rotate(%i,%i,%i)" % ( angle, x, y ))
self.addElement(e)
def writeGrid(self):
"""add grid lines."""
middlex = self.mDataMiddleX
middley = self.mDataMiddleY
# print separators
for c in range(len(self.contigs)):
contig = self.contigs[c]
pos = self.getPosition(contig, "+", 0)
angle = self.getAngle(pos)
x, y = self.getPosOnArc(angle, self.mRadius)
e = SVGdraw.line(middlex,
middley,
x,
y,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=self.mGridStrokeWidth)
self.addElement(e, self.mPlaneGrid)
if c < len(self.contigs) - 1:
next_angle = self.getAngle(
self.getPosition(self.contigs[c + 1], "+", 0))
else:
next_angle = 360
x, y = self.getPosOnArc(
angle + float(next_angle - angle) / 2, self.mRadiusStart / 2)
e = SVGdraw.text(x,
y,
contig,
self.mGridFontSize,
self.mGridFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
# do not rotate text:
# transform="rotate(%i,%i,%i)" % ( angle, x, y ))
self.addElement(e)
def plotLinksForPair(self, species1, species2, colour=BLACK, plane=0):
"""plot links."""
if species1 not in self.mOrthologs or species2 not in self.mOrthologs:
return
for group1 in self.mOrthologs[species1]:
if group1 in self.mOrthologs[species2]:
for g1 in self.mOrthologs[species1][group1]:
for g2 in self.mOrthologs[species2][group1]:
x1, y1 = self.mMapGene2Coord[g1]
x2, y2 = self.mMapGene2Coord[g2]
e = SVGdraw.line(
x1,
y1,
x2,
y2,
stroke="rgb(%i,%i,%i)" % colour,
)
self.addElement(e, plane=plane)
def writeGrid(self):
"""add grid lines."""
# print last circle
self.mRadius = self.mRadiusMax + self.mRadiusIncrement
self.addSeparator()
# print separators
for contig, pos in self.contig2Position.items():
pos = self.getPosition(contig, "+", 0)
angle = self.getAngle(pos)
x, y = self.getPosOnArc(angle, self.mRadius)
e = SVGdraw.line(self.mDataMiddleX,
self.mDataMiddleY,
x,
y,
stroke="rgb(%i,%i,%i)" % BLACK)
self.addElement(e, self.mPlaneGrid)
x, y = self.getPosOnArc(
angle, (self.mRadius + self.mRadiusStart) / 2)
e = SVGdraw.text(x,
y,
contig,
self.mHeaderFontSize,
self.mHeaderFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start",
transform="rotate(%i,%i,%i)" % (angle, x, y))
self.addElement(e)
def writeGrid(self):
"""add grid lines."""
# print last circle
self.mRadius = self.mRadiusMax + self.mRadiusIncrement
self.addSeparator()
# print separators
for contig, pos in self.contig2Position.items():
pos = self.getPosition(contig, "+", 0)
angle = self.getAngle(pos)
x, y = self.getPosOnArc(angle, self.mRadius)
e = SVGdraw.line(self.mDataMiddleX,
self.mDataMiddleY,
x,
y,
stroke="rgb(%i,%i,%i)" % BLACK)
self.addElement(e, self.mPlaneGrid)
x, y = self.getPosOnArc(angle,
(self.mRadius + self.mRadiusStart) / 2)
e = SVGdraw.text(x,
y,
contig,
self.mHeaderFontSize,
self.mHeaderFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start",
transform="rotate(%i,%i,%i)" % (angle, x, y))
self.addElement(e)
def addDuplication(self,
entries,
map_gene2pos,
height,
url=None,
with_separator=True,
link_to_previous=False,
quality2symbol={},
quality2mask={}):
"""add a dot in row/col."""
mi, ma = None, 0
pos = bisect.bisect(self.mColourThresholds, height)
master_colour = self.mColours[pos]
chrs = {}
points = []
for species, transcript, gene, quality in entries:
chr, strand, first_res, last_res = map_gene2pos[gene]
chrs[chr] = 1
pos1 = self.getPosition(chr, strand, first_res)
pos2 = self.getPosition(chr, strand, last_res)
a = min(pos1, pos2)
b = max(pos1, pos2)
if mi is None:
mi = a
else:
mi = min(a, mi)
ma = max(b, ma)
points.append((pos1, pos2, gene, quality))
# decide whether we need to increment the radius
cis = len(chrs) == 1
old_radius = self.mRadius
is_overlap = False
if cis:
if not self.mLastChr:
self.mLastChr = chr
if chr != self.mLastChr:
self.mRadius = self.mRadiusFallBack
self.mLastMax = ma
self.mPreviousMax = ma
self.mLastChr = chr
else:
if self.mPreviousMax + self.mMinDistance > mi:
# overlap due to close proximitiy
self.mRadius += self.mRadiusIncrement
if with_separator:
self.addSeparator()
# true overlap
if self.mPreviousMax > mi:
is_overlap = True
elif self.mLastMax + self.mMinDistance > mi:
pass
else:
self.mRadius = self.mRadiusFallBack
self.mLastMax = max(self.mLastMax, ma)
else:
if self.mLastMax > mi:
self.mRadius += self.mRadiusIncrement
if with_separator:
self.addSeparator()
if cis and self.mPreviousCis and (link_to_previous or is_overlap):
# print old_x1, old_y1, old_x2, old_y2, new_x1, new_y2, new_x2,
# new_y2
r1 = old_radius
r2 = self.mRadius
old_x1, old_y1 = self.getPosOnArcForRadius(self.mPreviousMin, r1)
old_x2, old_y2 = self.getPosOnArcForRadius(self.mPreviousMax, r1)
new_x1, new_y1 = self.getPosOnArcForRadius(mi, r2)
new_x2, new_y2 = self.getPosOnArcForRadius(ma, r2)
if link_to_previous:
# print cis, entries, chrs
d = SVGdraw.pathdata(old_x1, old_y1)
d.ellarc(r1, r1, 0, 0, 1, old_x2, old_y2)
d.line(new_x2, new_y2)
d.ellarc(r2, r2, 0, 0, 1, new_x1, new_y1)
d.line(old_x1, old_y1)
e = SVGdraw.path(d,
fill="rgb(%i,%i,%i)" % GREY,
stroke="rgb(%i,%i,%i)" % GREY,
stroke_width=1)
else:
# get points of center
old_x1, old_y1 = self.getPosOnArcForRadius(
(self.mPreviousMax + self.mPreviousMin) / 2, r1)
new_x1, new_y1 = self.getPosOnArcForRadius((ma + mi) / 2, r2)
# lines for interleaved spans: skip
if not ((self.mPreviousMin < mi and self.mPreviousMax > ma) or
(self.mPreviousMin > mi and self.mPreviousMax < ma)):
## d = SVGdraw.pathdata( old_x2, old_y2 )
## d.line( new_x2, new_y2 )
## d.move( new_x1, new_y1 )
## d.line( old_x1, old_y1 )
## d.move( old_x2, old_y2 )
# e = SVGdraw.path( d,
## fill = "none",
## stroke = "rgb(%i,%i,%i)" % BLACK,
# stroke_width = self.mMarkerWidth / 2 )
e = SVGdraw.line(old_x1,
old_y1,
new_x1,
new_y1,
fill="none",
stroke="rgb(%i,%i,%i)" % GREY,
stroke_width=self.mMarkerWidth / 2)
else:
# lines for covering spans, as these overlaps
e = None
# e = SVGdraw.line( old_x1, old_y1,
## new_x1, new_y1,
## fill = "none",
## stroke = "rgb(%i,%i,%i)" % GREY,
# stroke_width = self.mMarkerWidth / 2 )
if e:
self.addElement(e, self.mPlaneJoins)
self.mPreviousMin = mi
self.mPreviousMax = ma
self.mPreviousCis = cis
self.mRadiusMax = max(self.mRadius, self.mRadiusMax)
# draw points
link_colour = master_colour
link_width = 10
for pos1, pos2, gene, quality in points:
angle = self.getAngle((pos1 + pos2) / 2)
x, y = self.getPosOnArc(angle, self.mRadius)
try:
symbol = quality2symbol[quality]
except KeyError:
symbol = "rect"
if quality in quality2mask:
colour = GREY
link_colour = GREY
link_width = 1
else:
colour = master_colour
if symbol == "circle":
ee = SVGdraw.circle(x,
y,
self.mMarkerWidth,
fill="rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width=1)
elif symbol == "rect":
ee = SVGdraw.rect(x - self.mMarkerWidth / 2,
y - self.mMarkerWidth / 2,
self.mMarkerWidth,
self.mMarkerWidth,
fill="rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width=1)
if url:
e = SVGdraw.link(url % gene)
e.addElement(ee)
else:
e = ee
self.addElement(e)
angle1 = self.getAngle(mi)
angle2 = self.getAngle(ma)
x1, y1 = self.getPosOnArc(angle1, self.mRadius)
x2, y2 = self.getPosOnArc(angle2, self.mRadius)
d = SVGdraw.pathdata(x1, y1)
if cis:
d.ellarc(self.mRadius, self.mRadius, 0, 0, 1, x2, y2)
else:
d.ellarc(self.mRadius * 2, self.mRadius * 2, 0, 0, 0, x2, y2)
e = SVGdraw.path(d,
fill="none",
stroke="rgb(%i,%i,%i)" % link_colour,
stroke_width=link_width)
self.addElement(e)
def addDuplication( self, entries, map_gene2pos, height,
url = None,
with_separator=True,
link_to_previous = False,
quality2symbol = {},
quality2mask = {}):
"""add a dot in row/col."""
mi, ma = None, 0
pos = bisect.bisect( self.mColourThresholds, height )
master_colour = self.mColours[pos]
chrs = {}
points = []
for species, transcript, gene, quality in entries:
chr, strand, first_res, last_res = map_gene2pos[gene]
chrs[chr] = 1
pos1 = self.getPosition( chr, strand, first_res )
pos2 = self.getPosition( chr, strand, last_res )
a = min( pos1, pos2 )
b = max( pos1, pos2 )
if mi == None:
mi = a
else:
mi = min(a, mi)
ma = max(b, ma)
points.append( (pos1, pos2, gene, quality) )
## decide whether we need to increment the radius
cis = len(chrs) == 1
old_radius = self.mRadius
is_overlap = False
if cis:
if not self.mLastChr:
self.mLastChr = chr
if chr != self.mLastChr:
self.mRadius = self.mRadiusFallBack
self.mLastMax = ma
self.mPreviousMax = ma
self.mLastChr = chr
else:
if self.mPreviousMax + self.mMinDistance > mi:
## overlap due to close proximitiy
self.mRadius += self.mRadiusIncrement
if with_separator: self.addSeparator()
## true overlap
if self.mPreviousMax > mi:
is_overlap = True
elif self.mLastMax + self.mMinDistance > mi:
pass
else:
self.mRadius = self.mRadiusFallBack
self.mLastMax = max(self.mLastMax, ma)
else:
if self.mLastMax > mi:
self.mRadius += self.mRadiusIncrement
if with_separator: self.addSeparator()
if cis and self.mPreviousCis and (link_to_previous or is_overlap):
# print old_x1, old_y1, old_x2, old_y2, new_x1, new_y2, new_x2, new_y2
r1 = old_radius
r2 = self.mRadius
old_x1, old_y1 = self.getPosOnArcForRadius( self.mPreviousMin, r1 )
old_x2, old_y2 = self.getPosOnArcForRadius( self.mPreviousMax, r1 )
new_x1, new_y1 = self.getPosOnArcForRadius( mi, r2 )
new_x2, new_y2 = self.getPosOnArcForRadius( ma, r2 )
if link_to_previous:
# print cis, entries, chrs
d = SVGdraw.pathdata( old_x1, old_y1 )
d.ellarc( r1, r1, 0, 0, 1, old_x2, old_y2 )
d.line( new_x2, new_y2 )
d.ellarc( r2, r2, 0, 0, 1, new_x1, new_y1 )
d.line( old_x1, old_y1 )
e = SVGdraw.path( d,
fill = "rgb(%i,%i,%i)" % GREY,
stroke = "rgb(%i,%i,%i)" % GREY,
stroke_width = 1 )
else:
# get points of center
old_x1, old_y1 = self.getPosOnArcForRadius( (self.mPreviousMax + self.mPreviousMin) / 2, r1 )
new_x1, new_y1 = self.getPosOnArcForRadius( (ma + mi) / 2, r2 )
# lines for interleaved spans: skip
if not ((self.mPreviousMin < mi and self.mPreviousMax > ma) or \
(self.mPreviousMin > mi and self.mPreviousMax < ma)) :
## d = SVGdraw.pathdata( old_x2, old_y2 )
## d.line( new_x2, new_y2 )
## d.move( new_x1, new_y1 )
## d.line( old_x1, old_y1 )
## d.move( old_x2, old_y2 )
## e = SVGdraw.path( d,
## fill = "none",
## stroke = "rgb(%i,%i,%i)" % BLACK,
## stroke_width = self.mMarkerWidth / 2 )
e = SVGdraw.line( old_x1, old_y1,
new_x1, new_y1,
fill = "none",
stroke = "rgb(%i,%i,%i)" % GREY,
stroke_width = self.mMarkerWidth / 2 )
else:
# lines for covering spans, as these overlaps
e = None
## e = SVGdraw.line( old_x1, old_y1,
## new_x1, new_y1,
## fill = "none",
## stroke = "rgb(%i,%i,%i)" % GREY,
## stroke_width = self.mMarkerWidth / 2 )
if e:
self.addElement( e, self.mPlaneJoins )
self.mPreviousMin = mi
self.mPreviousMax = ma
self.mPreviousCis = cis
self.mRadiusMax = max(self.mRadius, self.mRadiusMax)
## draw points
link_colour = master_colour
link_width = 10
for pos1, pos2, gene, quality in points:
angle = self.getAngle( (pos1 + pos2) / 2 )
x,y = self.getPosOnArc( angle, self.mRadius )
try:
symbol = quality2symbol[quality]
except KeyError:
symbol = "rect"
if quality in quality2mask:
colour = GREY
link_colour = GREY
link_width = 1
else:
colour = master_colour
if symbol == "circle":
ee = SVGdraw.circle( x, y, self.mMarkerWidth,
fill = "rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width= 1)
elif symbol == "rect":
ee = SVGdraw.rect( x-self.mMarkerWidth/2, y-self.mMarkerWidth/2,
self.mMarkerWidth, self.mMarkerWidth,
fill = "rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width= 1)
if url:
e = SVGdraw.link( url % gene )
e.addElement( ee )
else:
e = ee
self.addElement( e )
angle1 = self.getAngle( mi )
angle2 = self.getAngle( ma )
x1,y1 = self.getPosOnArc( angle1, self.mRadius )
x2,y2 = self.getPosOnArc( angle2, self.mRadius )
d = SVGdraw.pathdata( x1, y1 )
if cis:
d.ellarc( self.mRadius, self.mRadius, 0, 0, 1, x2, y2 )
else:
d.ellarc( self.mRadius * 2, self.mRadius * 2, 0, 0, 0, x2, y2 )
e = SVGdraw.path( d,
fill = "none",
stroke = "rgb(%i,%i,%i)" % link_colour,
stroke_width = link_width )
self.addElement(e)
def writeFooter(self):
"""write footer.
The footer contains the legend.
"""
total_branch_length = (
max(self.mNodeWidthsEnd) - min(self.mNodeWidthsStart)) / self.mBranchScaleFactor
self.mFooterX = self.getHeaderWidth()
self.mFooterY = self.getHeaderHeight(
) + self.mDataHeight + self.mSeparatorHeight
ruler_start = self.mFooterX
ruler_end = self.mFooterX + \
int(total_branch_length * self.mBranchScaleFactor)
if "ruler" in self.mRulerElements:
# full length ruler with tick marks and labels
e = SVGdraw.line(ruler_start,
self.mFooterY + self.mRulerTickSize + 1,
ruler_end,
self.mFooterY + self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
# get reasonable intervalls
increment = self.mRulerIncrement * self.mBranchScaleFactor
# adjust increment for extremely long trees
if (ruler_end - ruler_start) / increment > 1000:
increment = (ruler_end - ruler_start) / 1000.0
self.mRulerIncrement = increment / self.mBranchScaleFactor
if "right-ticks" in self.mRulerElements:
x = ruler_end
while x >= ruler_start:
e = SVGdraw.line(x,
self.mFooterY,
x,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
x -= self.mRulerIncrement * self.mBranchScaleFactor
self.mFooterY += 2 * self.mRulerTickSize + \
1 + self.mSeparatorHeight
if "left-ticks" in self.mRulerElements:
x = ruler_start
while x <= ruler_end:
e = SVGdraw.line(x,
self.mFooterY,
x,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
x += increment
self.mFooterY += 2 * self.mRulerTickSize + \
1 + self.mSeparatorHeight
if "scale" in self.mRulerElements:
w = int(self.mRulerIncrement * self.mBranchScaleFactor)
e = SVGdraw.line(ruler_end,
self.mFooterY + self.mRulerTickSize + 1,
ruler_end - w,
self.mFooterY + self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
e = SVGdraw.line(ruler_end,
self.mFooterY,
ruler_end,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
e = SVGdraw.line(ruler_end - w,
self.mFooterY,
ruler_end - w,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
e = SVGdraw.text(ruler_end - w / 2,
self.mFooterY + 2 * self.mRulerTickSize +
1 + self.mRulerFontSize,
self.mRulerFormat % self.mRulerIncrement,
self.mRulerFontSize,
self.mRulerFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
self.addElement(e)
self.mFooterY += 2 * self.mRulerTickSize + 1 + self.mRulerFontSize
e, self.mFooterX, self.mFooterY = self.mDecoratorExternalNodes.getLegend(
self.mFooterX, self.mFooterY)
self.addElements(e)
e, self.mFooterX, self.mFooterY = self.mDecoratorInternalNodes.getLegend(
self.mFooterX, self.mFooterY)
self.addElements(e)
def writeFooter(self):
"""write footer.
The footer contains the legend.
"""
total_branch_length = (max(self.mNodeWidthsEnd) - min(
self.mNodeWidthsStart)) / self.mBranchScaleFactor
self.mFooterX = self.getHeaderWidth()
self.mFooterY = self.getHeaderHeight(
) + self.mDataHeight + self.mSeparatorHeight
ruler_start = self.mFooterX
ruler_end = self.mFooterX + \
int(total_branch_length * self.mBranchScaleFactor)
if "ruler" in self.mRulerElements:
# full length ruler with tick marks and labels
e = SVGdraw.line(ruler_start,
self.mFooterY + self.mRulerTickSize + 1,
ruler_end,
self.mFooterY + self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
# get reasonable intervalls
increment = self.mRulerIncrement * self.mBranchScaleFactor
# adjust increment for extremely long trees
if (ruler_end - ruler_start) / increment > 1000:
increment = (ruler_end - ruler_start) / 1000.0
self.mRulerIncrement = increment / self.mBranchScaleFactor
if "right-ticks" in self.mRulerElements:
x = ruler_end
while x >= ruler_start:
e = SVGdraw.line(x,
self.mFooterY,
x,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
x -= self.mRulerIncrement * self.mBranchScaleFactor
self.mFooterY += 2 * self.mRulerTickSize + \
1 + self.mSeparatorHeight
if "left-ticks" in self.mRulerElements:
x = ruler_start
while x <= ruler_end:
e = SVGdraw.line(x,
self.mFooterY,
x,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
x += increment
self.mFooterY += 2 * self.mRulerTickSize + \
1 + self.mSeparatorHeight
if "scale" in self.mRulerElements:
w = int(self.mRulerIncrement * self.mBranchScaleFactor)
e = SVGdraw.line(ruler_end,
self.mFooterY + self.mRulerTickSize + 1,
ruler_end - w,
self.mFooterY + self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
e = SVGdraw.line(ruler_end,
self.mFooterY,
ruler_end,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
e = SVGdraw.line(ruler_end - w,
self.mFooterY,
ruler_end - w,
self.mFooterY + 2 * self.mRulerTickSize + 1,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(e)
e = SVGdraw.text(ruler_end - w / 2,
self.mFooterY + 2 * self.mRulerTickSize + 1 +
self.mRulerFontSize,
self.mRulerFormat % self.mRulerIncrement,
self.mRulerFontSize,
self.mRulerFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
self.addElement(e)
self.mFooterY += 2 * self.mRulerTickSize + 1 + self.mRulerFontSize
e, self.mFooterX, self.mFooterY = self.mDecoratorExternalNodes.getLegend(
self.mFooterX, self.mFooterY)
self.addElements(e)
e, self.mFooterX, self.mFooterY = self.mDecoratorInternalNodes.getLegend(
self.mFooterX, self.mFooterY)
self.addElements(e)
