def addValue(self, row, col, size, colour_value):
"""add a dot in row/col.
"""
# decide the size of the box
pos = bisect.bisect(self.mThresholdsSize, size)
if self.mRevertSize:
size = self.mMaxBoxSize * \
(1.0 - float(pos) / len(self.mThresholdsSize))
else:
size = self.mMaxBoxSize * float(pos) / len(self.mThresholdsSize)
d = (self.mMaxBoxSize - size) / 2
x = self.mMapCol2Position[col] + d
try:
y = self.mMapRow2Position[row] + d
except KeyError:
return
# determine the colour of the box
pos = bisect.bisect(self.mThresholdsColour, colour_value)
colour = self.mColours[pos]
e = SVGdraw.rect(x,
y,
size,
size,
stroke="black",
fill="rgb(%i,%i,%i)" % colour)
self.mElements.append(e)
def addValue(self, row, col, size, colour_value):
"""add a dot in row/col.
"""
# decide the size of the box
pos = bisect.bisect(self.mThresholdsSize, size)
if self.mRevertSize:
size = self.mMaxBoxSize * \
(1.0 - float(pos) / len(self.mThresholdsSize))
else:
size = self.mMaxBoxSize * float(pos) / len(self.mThresholdsSize)
d = (self.mMaxBoxSize - size) / 2
x = self.mMapCol2Position[col] + d
try:
y = self.mMapRow2Position[row] + d
except KeyError:
return
# determine the colour of the box
pos = bisect.bisect(self.mThresholdsColour, colour_value)
colour = self.mColours[pos]
e = SVGdraw.rect(x, y,
size, size,
stroke="black",
fill="rgb(%i,%i,%i)" % colour)
self.mElements.append(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 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, x, y, map_node2height):
elements = []
for n in self.mTree.get_terminals():
t = self.mTree.node(n).data.taxon
if t not in self.mMapId2Cluster:
continue
cluster = self.mMapId2Cluster[t]
if cluster not in self.mMapCluster2Colour:
self.mMapCluster2Colour[cluster] = COLOURS[
len(self.mMapCluster2Colour) % len(COLOURS)]
colour = self.mMapCluster2Colour[cluster]
elements.append(SVGdraw.rect(x, y + map_node2height[n] - self.mBoxWidth / 2, self.mBoxWidth, self.mBoxWidth,
stroke="rgb(%i,%i,%i)" % colour,
fill="rgb(%i,%i,%i)" % colour))
return elements
def getElements(self, node_id, x, y):
e = []
colour = self.getColour(node_id, x, y)
if self.mPlotSymbol == "circle":
e.append(SVGdraw.circle(x + self.mFontSize / 2,
y,
self.mFontSize / 2,
stroke="rgb(%i,%i,%i)" % BLACK,
fill="rgb(%i,%i,%i)" % colour))
elif self.mPlotSymbol == "square":
e.append(SVGdraw.rect(x, y - self.mFontSize / 2,
self.mFontSize,
self.mFontSize,
stroke="rgb(%i,%i,%i)" % BLACK,
fill="rgb(%i,%i,%i)" % colour))
return e
def getElements(self, node_id, x, y):
e = []
colour = self.getColour(node_id, x, y)
if self.mPlotSymbol == "circle":
e.append(
SVGdraw.circle(x + self.mFontSize / 2,
y,
self.mFontSize / 2,
stroke="rgb(%i,%i,%i)" % BLACK,
fill="rgb(%i,%i,%i)" % colour))
elif self.mPlotSymbol == "square":
e.append(
SVGdraw.rect(x,
y - self.mFontSize / 2,
self.mFontSize,
self.mFontSize,
stroke="rgb(%i,%i,%i)" % BLACK,
fill="rgb(%i,%i,%i)" % colour))
return e
def getElements(self, x, y, map_node2height):
elements = []
for n in self.mTree.get_terminals():
t = self.mTree.node(n).data.taxon
if t not in self.mMapId2Cluster:
continue
cluster = self.mMapId2Cluster[t]
if cluster not in self.mMapCluster2Colour:
self.mMapCluster2Colour[cluster] = COLOURS[len(
self.mMapCluster2Colour) % len(COLOURS)]
colour = self.mMapCluster2Colour[cluster]
elements.append(
SVGdraw.rect(x,
y + map_node2height[n] - self.mBoxWidth / 2,
self.mBoxWidth,
self.mBoxWidth,
stroke="rgb(%i,%i,%i)" % colour,
fill="rgb(%i,%i,%i)" % colour))
return elements
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 plotGene(self, x, y, gene=None, group_id=None):
"""plot a gene at x,y."""
if gene:
group_id = gene.mOrthologId
colour, format = self.mMapGroup2Colour[group_id]
filled, shape = format.split("-")
if filled == "filled":
fill = "rgb(%i,%i,%i)" % colour
stroke = "rgb(%i,%i,%i)" % BLACK
stroke_width = 1
elif filled == "open":
fill = "rgb(%i,%i,%i)" % WHITE
stroke = "rgb(%i,%i,%i)" % colour
stroke_width = self.mBlockSize / 2
if shape == "circle":
ee = SVGdraw.circle(x, y, self.mBlockSize, fill=fill, stroke=stroke, stroke_width=stroke_width)
elif shape == "box":
ee = SVGdraw.rect(
x - self.mBlockSize,
y - self.mBlockSize,
2 * self.mBlockSize,
2 * self.mBlockSize,
fill=fill,
stroke=stroke,
stroke_width=stroke_width,
)
elif shape == "lefttriangle":
ee = SVGdraw.polygon(
(
(x - self.mBlockSize, y),
(x + self.mBlockSize, y - self.mBlockSize),
(x + self.mBlockSize, y + self.mBlockSize),
),
fill=fill,
stroke=stroke,
stroke_width=stroke_width,
)
elif shape == "righttriangle":
ee = SVGdraw.polygon(
(
(x - self.mBlockSize, y - self.mBlockSize),
(x + self.mBlockSize, y),
(x - self.mBlockSize, y + self.mBlockSize),
),
fill=fill,
stroke=stroke,
stroke_width=stroke_width,
)
elif shape == "uptriangle":
ee = SVGdraw.polygon(
(
(x, y - self.mBlockSize),
(x + self.mBlockSize, y + self.mBlockSize),
(x - self.mBlockSize, y + self.mBlockSize),
),
fill="rgb(%i,%i,%i)" % WHITE,
stroke="rgb(%i,%i,%i)" % colour,
stroke_width=self.mBlockSize / 2,
)
elif shape == "downtriangle":
ee = SVGdraw.polygon(
(
(x, y + self.mBlockSize),
(x + self.mBlockSize, y - self.mBlockSize),
(x - self.mBlockSize, y - self.mBlockSize),
),
fill="rgb(%i,%i,%i)" % WHITE,
stroke="rgb(%i,%i,%i)" % colour,
stroke_width=self.mBlockSize / 2,
)
return ee
def writeFooter(self):
"""write footer.
The footer contains the legend.
"""
current_x = self.mFooterFrom
current_y = self.mHeaderHeight + self.mDataHeight + 2 * self.mSeparator
###########################################################
# Draw legend 1: size of boxes
e = SVGdraw.text(current_x,
current_y + self.mFooterFontSize,
self.mThresholdsSizeTitle,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
current_x += len(self.mThresholdsSizeTitle) * \
self.mFooterFontSize / 1.5 + self.mSeparator
self.mElements.append(e)
l = len(self.mThresholdsSize)
for x in range(l):
if self.mRevertSize:
p = int(self.mMaxBoxSize * (1.0 - float(x) / l))
else:
p = int(self.mMaxBoxSize * (float(x) / l))
e = SVGdraw.rect(current_x,
current_y + (self.mMaxBoxSize - p) / 2,
p,
p,
stroke="black",
fill="rgb(%i,%i,%i)" % self.startColour)
self.mElements.append(e)
current_x += self.mMaxBoxSize + self.mSeparator
t = "< %g" % (self.mThresholdsSize[x])
e = SVGdraw.text(current_x,
current_y + self.mFooterFontSize,
t,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
current_x += len(t) * self.mFooterFontSize / 1.5 + self.mSeparator
self.mElements.append(e)
###########################################################
# Draw legend 2: colour of boxes
current_x = self.mFooterFrom
current_y += max(self.mFooterFontSize, self.mMaxBoxSize) + \
self.mSeparator
e = SVGdraw.text(current_x,
current_y + self.mFooterFontSize,
self.mThresholdsColourTitle,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
current_x += len(self.mThresholdsColourTitle) * \
self.mFooterFontSize / 1.5 + self.mSeparator
self.mElements.append(e)
l = len(self.mThresholdsColour)
for x in range(l + 1):
p = self.mMaxBoxSize
if x < l:
t = "< %g" % (self.mThresholdsColour[x])
else:
t = "> %g" % (self.mThresholdsColour[x - 1])
e = SVGdraw.rect(current_x,
current_y,
p,
p,
stroke="black",
fill="rgb(%i,%i,%i)" % self.mColours[x])
self.mElements.append(e)
current_x += self.mMaxBoxSize + self.mSeparator
e = SVGdraw.text(current_x,
current_y + self.mFooterFontSize,
t,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
current_x += len(t) * self.mFooterFontSize / 1.5 + self.mSeparator
self.mElements.append(e)
###########################################################
if self.mMaxPValue is not None or self.mMaxQValue is not None:
current_y += max(self.mFooterFontSize / 1.5,
self.mMaxBoxSize) + self.mSeparator
a = []
if self.mMaxPValue:
a.append("P < %6.4f" % self.mMaxPValue)
if self.mMaxQValue:
a.append("FDR = %6.4f" % self.mMaxQValue)
e = SVGdraw.text(self.mPageWidth / 2,
current_y + self.mFooterFontSize,
" ".join(a),
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
###########################################################
if self.mFooter:
current_y += max(self.mFooterFontSize / 1.5,
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.mElements.append(e)
def writeFooter(self):
"""write footer.
The footer contains the legend.
"""
current_x = self.mFooterFrom
current_y = self.mHeaderHeight + self.mDataHeight + 2 * self.mSeparator
###########################################################
# Draw legend 1: size of boxes
e = SVGdraw.text(current_x,
current_y + self.mFooterFontSize,
self.mThresholdsSizeTitle,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
current_x += len(self.mThresholdsSizeTitle) * \
self.mFooterFontSize / 1.5 + self.mSeparator
self.mElements.append(e)
l = len(self.mThresholdsSize)
for x in range(l):
if self.mRevertSize:
p = int(self.mMaxBoxSize * (1.0 - float(x) / l))
else:
p = int(self.mMaxBoxSize * (float(x) / l))
e = SVGdraw.rect(current_x,
current_y + (self.mMaxBoxSize - p) / 2,
p, p,
stroke="black",
fill="rgb(%i,%i,%i)" % self.startColour)
self.mElements.append(e)
current_x += self.mMaxBoxSize + self.mSeparator
t = "< %g" % (self.mThresholdsSize[x])
e = SVGdraw.text(current_x,
current_y + self.mFooterFontSize,
t,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
current_x += len(t) * self.mFooterFontSize / 1.5 + self.mSeparator
self.mElements.append(e)
###########################################################
# Draw legend 2: colour of boxes
current_x = self.mFooterFrom
current_y += max(self.mFooterFontSize, self.mMaxBoxSize) + \
self.mSeparator
e = SVGdraw.text(current_x,
current_y + self.mFooterFontSize,
self.mThresholdsColourTitle,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
current_x += len(self.mThresholdsColourTitle) * \
self.mFooterFontSize / 1.5 + self.mSeparator
self.mElements.append(e)
l = len(self.mThresholdsColour)
for x in range(l + 1):
p = self.mMaxBoxSize
if x < l:
t = "< %g" % (self.mThresholdsColour[x])
else:
t = "> %g" % (self.mThresholdsColour[x - 1])
e = SVGdraw.rect(current_x,
current_y,
p, p,
stroke="black",
fill="rgb(%i,%i,%i)" % self.mColours[x])
self.mElements.append(e)
current_x += self.mMaxBoxSize + self.mSeparator
e = SVGdraw.text(current_x,
current_y + self.mFooterFontSize,
t,
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
current_x += len(t) * self.mFooterFontSize / 1.5 + self.mSeparator
self.mElements.append(e)
###########################################################
if self.mMaxPValue is not None or self.mMaxQValue is not None:
current_y += max(self.mFooterFontSize / 1.5,
self.mMaxBoxSize) + self.mSeparator
a = []
if self.mMaxPValue:
a.append("P < %6.4f" % self.mMaxPValue)
if self.mMaxQValue:
a.append("FDR = %6.4f" % self.mMaxQValue)
e = SVGdraw.text(self.mPageWidth / 2,
current_y + self.mFooterFontSize,
" ".join(a),
self.mFooterFontSize,
self.mFooterFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
###########################################################
if self.mFooter:
current_y += max(self.mFooterFontSize / 1.5,
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.mElements.append(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 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 = []
if not link_to_previous:
self.mPreviousPoints = {}
########################################################
########################################################
########################################################
# convert gene list to a set of 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, chr))
########################################################
########################################################
########################################################
# 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()
self.mPreviousMin = mi
self.mPreviousMax = ma
self.mPreviousCis = cis
self.mRadiusMax = max(self.mRadius, self.mRadiusMax)
########################################################
########################################################
########################################################
# draw points
########################################################
link_colour = master_colour
link_rad_width = self.mLinkRadStrokeWidth
link_arc_width = self.mLinkArcStrokeWidth
new_points = {}
for pos1, pos2, gene, quality, chr 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 = self.mLinkColourSymbolMasked
link_colour = self.mLinkColourMasked
link_rad_width = self.mLinkStrokeWidthMasked
link_arc_width = self.mLinkStrokeWidthMasked
else:
colour = master_colour
if gene in self.mPreviousPoints:
continue
new_points[gene] = (x, y, angle, quality, chr)
if symbol == "circle":
ee = SVGdraw.circle(x, y, self.mLinkSymbolSize,
fill="rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width=self.mLinkStrokeWidthSymbol)
elif symbol == "rect":
ee = SVGdraw.rect(x - self.mLinkSymbolSize / 2, y - self.mLinkSymbolSize / 2,
self.mLinkSymbolSize, self.mLinkSymbolSize,
fill="rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width=self.mLinkStrokeWidthSymbol)
if url:
e = SVGdraw.link(url % gene)
e.addElement(ee)
else:
e = ee
self.addWheelElement(e)
########################################################
########################################################
########################################################
# write all arcs in between old points and new points
# cis: circular arc
# trans: radial arc
########################################################
angles = []
for x1, y1, angle1, quality1, chr1 in new_points.values():
# reduce clutter by not writing arc to the same angle
for x2, y2, angle2, quality2, chr2 in self.mPreviousPoints.values():
for a in angles:
if a - self.mAngleResolution < angle2 < a + self.mAngleResolution:
break
else:
angles.append(angle2)
d = SVGdraw.pathdata(x1, y1)
if chr1 == chr2:
d.relellarc(
self.mRadius, self.mRadius, 0, 0, 1, x2 - x1, y2 - y1)
link_width = link_rad_width
else:
d.relellarc(
self.mRadius * 2, self.mRadius * 2, 0, 0, 0, x2 - x1, y2 - y1)
link_width = link_arc_width
e = SVGdraw.path(d,
fill="none",
stroke="rgb(%i,%i,%i)" % link_colour,
stroke_width=link_width)
self.addWheelElement(e, self.mPlaneLinks)
# plot lines between new points
new_genes = new_points.keys()
for g1 in range(len(new_genes) - 1):
x1, y1, angle1, quality1, chr1 = new_points[new_genes[g1]]
for g2 in range(g1 + 1, len(new_genes)):
x2, y2, angle2, quality2, chr2 = new_points[new_genes[g2]]
for a in angles:
if a - self.mAngleResolution < angle2 < a + self.mAngleResolution:
break
else:
angles.append(angle2)
d = SVGdraw.pathdata(x1, y1)
if chr1 == chr2:
d.relellarc(
self.mRadius, self.mRadius, 0, 0, 1, x2 - x1, y2 - y1)
link_width = link_rad_width
else:
d.relellarc(
self.mRadius * 2, self.mRadius * 2, 0, 0, 0, x2 - x1, y2 - y1)
link_width = link_arc_width
e = SVGdraw.path(d,
fill="none",
stroke="rgb(%i,%i,%i)" % link_colour,
stroke_width=link_width)
self.addWheelElement(e, self.mPlaneLinks)
# add new points to old points
for k, v in new_points.items():
self.mPreviousPoints[k] = v
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 = []
if not link_to_previous:
self.mPreviousPoints = {}
########################################################
########################################################
########################################################
# convert gene list to a set of 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, chr))
########################################################
########################################################
########################################################
# 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()
self.mPreviousMin = mi
self.mPreviousMax = ma
self.mPreviousCis = cis
self.mRadiusMax = max(self.mRadius, self.mRadiusMax)
########################################################
########################################################
########################################################
# draw points
########################################################
link_colour = master_colour
link_rad_width = self.mLinkRadStrokeWidth
link_arc_width = self.mLinkArcStrokeWidth
new_points = {}
for pos1, pos2, gene, quality, chr 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 = self.mLinkColourSymbolMasked
link_colour = self.mLinkColourMasked
link_rad_width = self.mLinkStrokeWidthMasked
link_arc_width = self.mLinkStrokeWidthMasked
else:
colour = master_colour
if gene in self.mPreviousPoints:
continue
new_points[gene] = (x, y, angle, quality, chr)
if symbol == "circle":
ee = SVGdraw.circle(x, y, self.mLinkSymbolSize,
fill="rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width=self.mLinkStrokeWidthSymbol)
elif symbol == "rect":
ee = SVGdraw.rect(x - self.mLinkSymbolSize / 2, y - self.mLinkSymbolSize / 2,
self.mLinkSymbolSize, self.mLinkSymbolSize,
fill="rgb(%i,%i,%i)" % colour,
stroke="black",
stroke_width=self.mLinkStrokeWidthSymbol)
if url:
e = SVGdraw.link(url % gene)
e.addElement(ee)
else:
e = ee
self.addWheelElement(e)
########################################################
########################################################
########################################################
# write all arcs in between old points and new points
# cis: circular arc
# trans: radial arc
########################################################
angles = []
for x1, y1, angle1, quality1, chr1 in new_points.values():
# reduce clutter by not writing arc to the same angle
for x2, y2, angle2, quality2, chr2 in self.mPreviousPoints.values():
for a in angles:
if a - self.mAngleResolution < angle2 < a + self.mAngleResolution:
break
else:
angles.append(angle2)
d = SVGdraw.pathdata(x1, y1)
if chr1 == chr2:
d.relellarc(
self.mRadius, self.mRadius, 0, 0, 1, x2 - x1, y2 - y1)
link_width = link_rad_width
else:
d.relellarc(
self.mRadius * 2, self.mRadius * 2, 0, 0, 0, x2 - x1, y2 - y1)
link_width = link_arc_width
e = SVGdraw.path(d,
fill="none",
stroke="rgb(%i,%i,%i)" % link_colour,
stroke_width=link_width)
self.addWheelElement(e, self.mPlaneLinks)
# plot lines between new points
new_genes = new_points.keys()
for g1 in range(len(new_genes) - 1):
x1, y1, angle1, quality1, chr1 = new_points[new_genes[g1]]
for g2 in range(g1 + 1, len(new_genes)):
x2, y2, angle2, quality2, chr2 = new_points[new_genes[g2]]
for a in angles:
if a - self.mAngleResolution < angle2 < a + self.mAngleResolution:
break
else:
angles.append(angle2)
d = SVGdraw.pathdata(x1, y1)
if chr1 == chr2:
d.relellarc(
self.mRadius, self.mRadius, 0, 0, 1, x2 - x1, y2 - y1)
link_width = link_rad_width
else:
d.relellarc(
self.mRadius * 2, self.mRadius * 2, 0, 0, 0, x2 - x1, y2 - y1)
link_width = link_arc_width
e = SVGdraw.path(d,
fill="none",
stroke="rgb(%i,%i,%i)" % link_colour,
stroke_width=link_width)
self.addWheelElement(e, self.mPlaneLinks)
# add new points to old points
for k, v in new_points.items():
self.mPreviousPoints[k] = v
def plotGene(self, x, y, gene=None, group_id=None):
"""plot a gene at x,y."""
if gene:
group_id = gene.mOrthologId
colour, format = self.mMapGroup2Colour[group_id]
filled, shape = format.split("-")
if filled == "filled":
fill = "rgb(%i,%i,%i)" % colour
stroke = "rgb(%i,%i,%i)" % BLACK
stroke_width = 1
elif filled == "open":
fill = "rgb(%i,%i,%i)" % WHITE
stroke = "rgb(%i,%i,%i)" % colour
stroke_width = self.mBlockSize / 2
if shape == "circle":
ee = SVGdraw.circle(x,
y,
self.mBlockSize,
fill=fill,
stroke=stroke,
stroke_width=stroke_width)
elif shape == "box":
ee = SVGdraw.rect(x - self.mBlockSize,
y - self.mBlockSize,
2 * self.mBlockSize,
2 * self.mBlockSize,
fill=fill,
stroke=stroke,
stroke_width=stroke_width)
elif shape == "lefttriangle":
ee = SVGdraw.polygon(((x - self.mBlockSize, y),
(x + self.mBlockSize, y - self.mBlockSize),
(x + self.mBlockSize, y + self.mBlockSize)),
fill=fill,
stroke=stroke,
stroke_width=stroke_width)
elif shape == "righttriangle":
ee = SVGdraw.polygon(((x - self.mBlockSize, y - self.mBlockSize),
(x + self.mBlockSize, y),
(x - self.mBlockSize, y + self.mBlockSize)),
fill=fill,
stroke=stroke,
stroke_width=stroke_width)
elif shape == "uptriangle":
ee = SVGdraw.polygon(((x, y - self.mBlockSize),
(x + self.mBlockSize, y + self.mBlockSize),
(x - self.mBlockSize, y + self.mBlockSize)),
fill="rgb(%i,%i,%i)" % WHITE,
stroke="rgb(%i,%i,%i)" % colour,
stroke_width=self.mBlockSize / 2)
elif shape == "downtriangle":
ee = SVGdraw.polygon(((x, y + self.mBlockSize),
(x + self.mBlockSize, y - self.mBlockSize),
(x - self.mBlockSize, y - self.mBlockSize)),
fill="rgb(%i,%i,%i)" % WHITE,
stroke="rgb(%i,%i,%i)" % colour,
stroke_width=self.mBlockSize / 2)
return ee
