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 writeToFile(self, outfile):
"""write svg image to file.
"""
self.finalizePlot()
self.mRoot = SVGdraw.drawing()
self.mDraw = SVGdraw.svg(
(0, 0, self.mPageWidth, self.mPageHeight), "100%", "100%")
kk = self.mElements.keys()
kk.sort()
kk.reverse()
for k in kk:
for e in self.mElements[k]:
self.mDraw.addElement(e)
self.mRoot.setSVG(self.mDraw)
tfile = tempfile.mktemp()
self.mRoot.toXml(tfile)
lines = open(tfile, "r").readlines()
outfile.write(string.join(lines, ""))
outfile.write("\n")
os.remove(tfile)
def writeToFile(self, outfile):
"""write svg image to file.
"""
self.finalizePlot()
self.mRoot = SVGdraw.drawing()
self.mDraw = SVGdraw.svg((0, 0, self.mPageWidth, self.mPageHeight),
"100%", "100%")
kk = self.mElements.keys()
kk.sort()
kk.reverse()
for k in kk:
for e in self.mElements[k]:
self.mDraw.addElement(e)
self.mRoot.setSVG(self.mDraw)
tfile = tempfile.mktemp()
self.mRoot.toXml(tfile)
lines = open(tfile, "r").readlines()
outfile.write(string.join(lines, ""))
outfile.write("\n")
os.remove(tfile)
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 writeToFile(self, outfile):
"""write svg image to file.
"""
self.finalizePlot()
kk = self.mElements.keys()
kk.sort()
kk.reverse()
# make sure the image size is ok
min_x, min_y, max_x, max_y = 0, 0, 0, 0
for k in kk:
for e in self.mElements[k]:
for x in ('x', 'x2', 'x1'):
if x in e.attributes:
v = e.attributes[x]
min_x = min(min_x, v)
max_x = max(max_x, v)
for y in ('y', 'y2', 'y1'):
if y in e.attributes:
v = e.attributes[y]
min_y = min(min_y, v)
max_y = max(max_y, v)
min_x, min_y = int(math.floor(min_x)), int(math.floor(min_y))
max_x, max_y = int(math.floor(max_x)), int(math.floor(max_y))
for k in kk:
for e in self.mElements[k]:
for x in ('x', 'x2', 'x1'):
if x in e.attributes:
e.attributes[x] -= min_x
for x in ('y', 'y2', 'y1'):
if y in e.attributes:
e.attributes[y] -= min_y
# now add all the elements
self.mRoot = SVGdraw.drawing()
self.mDraw = SVGdraw.svg(
(0, 0, self.mPageWidth - min_x, self.mPageHeight - min_y), "100%",
"100%")
for k in kk:
for e in self.mElements[k]:
self.mDraw.addElement(e)
self.mRoot.setSVG(self.mDraw)
tfile = tempfile.mktemp()
self.mRoot.toXml(tfile)
lines = open(tfile, "r").readlines()
outfile.write(string.join(lines, ""))
outfile.write("\n")
os.remove(tfile)
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 writeToFile(self, outfile):
"""write svg image to file.
"""
self.finalizePlot()
kk = self.mElements.keys()
kk.sort()
kk.reverse()
# make sure the image size is ok
min_x, min_y, max_x, max_y = 0, 0, 0, 0
for k in kk:
for e in self.mElements[k]:
for x in ('x', 'x2', 'x1'):
if x in e.attributes:
v = e.attributes[x]
min_x = min(min_x, v)
max_x = max(max_x, v)
for y in ('y', 'y2', 'y1'):
if y in e.attributes:
v = e.attributes[y]
min_y = min(min_y, v)
max_y = max(max_y, v)
min_x, min_y = int(math.floor(min_x)), int(math.floor(min_y))
max_x, max_y = int(math.floor(max_x)), int(math.floor(max_y))
for k in kk:
for e in self.mElements[k]:
for x in ('x', 'x2', 'x1'):
if x in e.attributes:
e.attributes[x] -= min_x
for x in ('y', 'y2', 'y1'):
if y in e.attributes:
e.attributes[y] -= min_y
# now add all the elements
self.mRoot = SVGdraw.drawing()
self.mDraw = SVGdraw.svg(
(0, 0, self.mPageWidth - min_x, self.mPageHeight - min_y), "100%", "100%")
for k in kk:
for e in self.mElements[k]:
self.mDraw.addElement(e)
self.mRoot.setSVG(self.mDraw)
tfile = tempfile.mktemp()
self.mRoot.toXml(tfile)
lines = open(tfile, "r").readlines()
outfile.write(string.join(lines, ""))
outfile.write("\n")
os.remove(tfile)
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 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 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 writeRowHeader(self):
"""write row header
The row header contains the species names
"""
x = 0
y = self.mHeaderHeight
max_l = 0
for species in self.mSpeciesList:
max_l = max(max_l,
len(species) * self.mHeaderFontSize) * self.mFontFactor
e = SVGdraw.text(x,
y,
species,
self.mHeaderFontSize,
self.mHeaderFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="left")
self.addElement(e)
y += self.mBlockSize + self.mHorizontalSeparator
self.mHeaderWidth = max_l
def writeRowHeader(self):
"""write row header
The row header contains the species names
"""
x = 0
y = self.mHeaderHeight
max_l = 0
for species in self.mSpeciesList:
max_l = max(max_l, len(species) * self.mHeaderFontSize) * self.mFontFactor
e = SVGdraw.text(
x,
y,
species,
self.mHeaderFontSize,
self.mHeaderFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="left",
)
self.addElement(e)
y += self.mBlockSize + self.mHorizontalSeparator
self.mHeaderWidth = max_l
def getSVG(self, xoffset, yoffset):
return SVGdraw.image(self.mFilename,
self.mX + xoffset,
self.mY + yoffset,
self.mWidth,
self.mHeight,
opacity=self.mOpacity)
def plotOrthologs(self):
"""plot orthologs orthologwise."""
# Do the plot
for ortholog_id in self.mOrthologs1.keys():
for o1 in self.mOrthologs1[ortholog_id]:
try:
x = self.getCoords1(o1)
except KeyError:
continue
for o2 in self.mOrthologs2[ortholog_id]:
try:
y = self.getCoords2(o2)
except KeyError:
continue
e = SVGdraw.circle(x, y,
self.mDotRadius,
fill="rgb(%i,%i,%i)" % BLACK,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(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 plotOrthologs(self):
"""plot orthologs orthologwise."""
# Do the plot
for ortholog_id in self.mOrthologs1.keys():
for o1 in self.mOrthologs1[ortholog_id]:
try:
x = self.getCoords1(o1)
except KeyError:
continue
for o2 in self.mOrthologs2[ortholog_id]:
try:
y = self.getCoords2(o2)
except KeyError:
continue
e = SVGdraw.circle(x,
y,
self.mDotRadius,
fill="rgb(%i,%i,%i)" % BLACK,
stroke="rgb(%i,%i,%i)" % BLACK,
stroke_width=1)
self.addElement(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 writeColHeaders(self):
"""write row headers."""
current_x = self.mColWidth / 2
current_y = self.mHeaderHeight
for i in range(len(self.mColNames)):
if self.mMarkColumns and self.mMarkColumns[i]:
color = BLUE
name = self.mColNames[i] + "*"
else:
color = BLACK
name = self.mColNames[i]
e = SVGdraw.text(current_x,
current_y,
name,
self.mHeaderFontSize,
self.mHeaderFont,
stroke="rgb(%i,%i,%i)" % color,
text_anchor="start",
transform="rotate(-45,%i,%i)" %
(current_x, current_y))
self.mElements.append(e)
current_x += self.mColWidth
def getSVG(self, xoffset, yoffset):
return SVGdraw.image(self.mFilename,
self.mX + xoffset,
self.mY + yoffset,
self.mWidth,
self.mHeight,
opacity=self.mOpacity)
def getElements(self, node_id, x1, x2, y):
e = SVGTree.BranchDecoratorHorizontal.getElements(
self, node_id, x1, x2, y)
table_id = str(int(self.mTree.node(node_id).data.branchlength))
if table_id not in self.mTables:
return e
startx = x1 + self.mFontSize
y = y + self.mFontSize
table, column_widths = self.mTables[
table_id], self.mColumnWidths[table_id]
font_weight = "bold"
for r, row in enumerate(table):
x = startx
for c, col in enumerate(row):
e.append(SVGdraw.text(x, y,
col,
20,
self.mFont,
stroke="rgb(%i,%i,%i)" % self.mFontColour,
font_weight=font_weight,
text_anchor="left"))
x += column_widths[c] * self.mFontSize // 2
y += self.mFontSize
font_weight = "normal"
return e
def writeColHeaders(self):
"""write row headers."""
current_x = self.mColWidth / 2
current_y = self.mHeaderHeight
for i in range(len(self.mColNames)):
if self.mMarkColumns and self.mMarkColumns[i]:
color = BLUE
name = self.mColNames[i] + "*"
else:
color = BLACK
name = self.mColNames[i]
e = SVGdraw.text(
current_x,
current_y,
name,
self.mHeaderFontSize,
self.mHeaderFont,
stroke="rgb(%i,%i,%i)" % color,
text_anchor="start",
transform="rotate(-45,%i,%i)" % (current_x, current_y))
self.mElements.append(e)
current_x += self.mColWidth
def addSeparator(self):
"""add separator on circles."""
if self.mRadius not in self.mSeparators:
e = SVGdraw.circle(self.mDataMiddleX, self.mDataMiddleY, self.mRadius, fill="none",
stroke="rgb(%i,%i,%i)" % self.mGridColour,
stroke_width=self.mGridStrokeWidth)
self.addWheelElement(e, self.mPlaneGrid)
self.mSeparators[self.mRadius] = 1
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 addSeparator(self):
"""add separator on circles."""
if self.mRadius not in self.mSeparators:
e = SVGdraw.circle(self.mDataMiddleX, self.mDataMiddleY, self.mRadius, fill="none",
stroke="rgb(%i,%i,%i)" % self.mGridColour,
stroke_width=self.mGridStrokeWidth)
self.addWheelElement(e, self.mPlaneGrid)
self.mSeparators[self.mRadius] = 1
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 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 getElements(self, node_id, x, y):
node = self.mTree.node(node_id)
e = []
p = node.data.support
if p == 1.0:
e.append(
SVGdraw.circle(x,
y,
self.mRadius,
stroke="rgb(%i,%i,%i)" % SVGTree.BLACK,
fill="rgb(%i,%i,%i)" % SVGTree.RED))
elif p > 0.0:
e.append(
SVGdraw.circle(x,
y,
self.mRadius,
stroke="rgb(%i,%i,%i)" % SVGTree.BLACK,
fill="rgb(%i,%i,%i)" % SVGTree.WHITE))
d = SVGdraw.pathdata(x, y)
d.line(x + self.mRadius, y)
angle = 360.0 * p
dx = self.mRadius * math.cos(math.radians(angle)) + x
dy = self.mRadius * math.sin(math.radians(angle)) + y
if p <= 0.5:
d.ellarc(self.mRadius, self.mRadius, 0, 0, 1, dx, dy)
else:
d.ellarc(self.mRadius, self.mRadius, 0, 1, 1, dx, dy)
e.append(
SVGdraw.path(d,
stroke="rgb(%i,%i,%i)" % SVGTree.RED,
fill="rgb(%i,%i,%i)" % SVGTree.RED,
stroke_width=self.mStrokeWidth))
else:
pass
return 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 getElements(self, node_id, x, y, x_label=None, y_label=None):
e = NodeDecorator.getElements(self, node_id, x, y)
if x_label is None:
x_label = x
if y_label is None:
y_label = y
t = self.mTree.node(node_id).data.taxon
species = self.mExtractSpecies(t)
if species not in self.mMapSpecies2Colour:
self.mMapSpecies2Colour[species] = COLOURS[len(
self.mMapSpecies2Colour) % len(COLOURS)]
if species in self.mMapSpecies2Name:
tx = re.sub(species, "%s" % self.mMapSpecies2Name[species], t)
else:
tx = t
colour = self.getColour(node_id, x, y)
if self.mPlotLabel:
ee = SVGdraw.text(x_label,
y_label,
tx,
self.mFontSize,
self.mFont,
stroke="rgb(%i,%i,%i)" % colour,
text_anchor="left")
if self.mMapTaxon2URL is not None:
url = self.mMapTaxon2URL(t)
if url:
l = SVGdraw.link(url)
l.addElement(ee)
e.append(l)
else:
e.append(ee)
else:
e.append(ee)
return e
def getElements(self, node_id, x, y, x_label=None, y_label=None):
e = NodeDecorator.getElements(self, node_id, x, y)
if x_label is None:
x_label = x
if y_label is None:
y_label = y
t = self.mTree.node(node_id).data.taxon
species = self.mExtractSpecies(t)
if species not in self.mMapSpecies2Colour:
self.mMapSpecies2Colour[species] = COLOURS[
len(self.mMapSpecies2Colour) % len(COLOURS)]
if species in self.mMapSpecies2Name:
tx = re.sub(species, "%s" % self.mMapSpecies2Name[species], t)
else:
tx = t
colour = self.getColour(node_id, x, y)
if self.mPlotLabel:
ee = SVGdraw.text(x_label, y_label,
tx,
self.mFontSize,
self.mFont,
stroke="rgb(%i,%i,%i)" % colour,
text_anchor="left")
if self.mMapTaxon2URL is not None:
url = self.mMapTaxon2URL(t)
if url:
l = SVGdraw.link(url)
l.addElement(ee)
e.append(l)
else:
e.append(ee)
else:
e.append(ee)
return 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, 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, 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 writeTitle(self):
"""write title into plot."""
if self.mTitle:
e = SVGdraw.text(self.mPageWidth / 2,
self.mTitleFontSize,
self.mTitle,
self.mTitleFontSize,
self.mTitleFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
self.addElement(e)
def writeTitle(self):
"""write title into plot."""
if self.mTitle:
e = SVGdraw.text(self.mPageWidth / 2,
self.mTitleFontSize,
self.mTitle,
self.mTitleFontSize,
self.mTitleFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
self.addElement(e)
def getElements(self, node_id, x, y):
node = self.mTree.node(node_id)
e = []
p = node.data.support
if p == 1.0:
e.append(SVGdraw.circle(x, y, self.mRadius,
stroke="rgb(%i,%i,%i)" % SVGTree.BLACK,
fill="rgb(%i,%i,%i)" % SVGTree.RED))
elif p > 0.0:
e.append(SVGdraw.circle(x, y, self.mRadius,
stroke="rgb(%i,%i,%i)" % SVGTree.BLACK,
fill="rgb(%i,%i,%i)" % SVGTree.WHITE))
d = SVGdraw.pathdata(x, y)
d.line(x + self.mRadius, y)
angle = 360.0 * p
dx = self.mRadius * math.cos(math.radians(angle)) + x
dy = self.mRadius * math.sin(math.radians(angle)) + y
if p <= 0.5:
d.ellarc(self.mRadius, self.mRadius, 0, 0, 1, dx, dy)
else:
d.ellarc(self.mRadius, self.mRadius, 0, 1, 1, dx, dy)
e.append(SVGdraw.path(d,
stroke="rgb(%i,%i,%i)" % SVGTree.RED,
fill="rgb(%i,%i,%i)" % SVGTree.RED,
stroke_width=self.mStrokeWidth))
else:
pass
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 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 writeFooter(self):
"""write footer.
The footer contains the legend.
"""
if self.mTitle:
e = SVGdraw.text(self.mPageWidth / 2,
self.mTitleFontSize,
self.mTitle,
self.mTitleFontSize,
self.mTitleFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
self.addElement(e)
def writeFooter(self):
"""write footer.
The footer contains the legend.
"""
if self.mTitle:
e = SVGdraw.text(self.mPageWidth / 2,
self.mTitleFontSize,
self.mTitle,
self.mTitleFontSize,
self.mTitleFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="middle")
self.addElement(e)
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 getElements(self, node_id, x, y, x_label=None, y_label=None):
e = NodeDecorator.getElements(self, node_id, x, y)
if x_label is None:
x_label = x
if y_label is None:
y_label = y
e.append(SVGdraw.text(x_label, y_label,
self.mTree.node(node_id).data.taxon,
self.mFontSize,
self.mFont,
stroke="rgb(%i,%i,%i)" % BLACK,
font_style=self.mFontStyle,
text_anchor="left"))
return e
def writeFooter(self):
"""write footer.
The footer contains the legend.
"""
x = self.mHeaderWidth + self.mBlockSize
group_ids = self.mMapGroup2Colour.keys()
group_ids.sort()
ncolumns = 10
l = int(math.ceil(len(group_ids) / float(ncolumns)))
max_d = 0
for a in range(0, ncolumns):
y = self.mHeaderHeight + self.mDataHeight
for b in range(a * l, min(len(group_ids), (a + 1) * l)):
group_id = group_ids[b]
e = self.plotGene(x, y, group_id=group_id)
self.addElement(e)
t = str(group_id)
max_d = max(
len(t) * self.mLegendFontSize * self.mFontFactor, max_d)
e = SVGdraw.text(x + self.mBlockSize +
self.mLegendVerticalSeparator,
y,
str(group_id),
self.mLegendFontSize,
self.mLegendFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="left")
self.addElement(e)
y += self.mLegendFontSize + self.mLegendHorizontalSeparator
x += max_d + 2 * self.mBlockSize + \
2 * self.mLegendVerticalSeparator
def getElements(self, node_id, x, y, x_label=None, y_label=None):
e = NodeDecorator.getElements(self, node_id, x, y)
if x_label is None:
x_label = x
if y_label is None:
y_label = y
e.append(
SVGdraw.text(x_label,
y_label,
self.mTree.node(node_id).data.taxon,
self.mFontSize,
self.mFont,
stroke="rgb(%i,%i,%i)" % BLACK,
font_style=self.mFontStyle,
text_anchor="left"))
return e
def writeFooter(self):
"""write footer.
The footer contains the legend.
"""
x = self.mHeaderWidth + self.mBlockSize
group_ids = self.mMapGroup2Colour.keys()
group_ids.sort()
ncolumns = 10
l = int(math.ceil(len(group_ids) / float(ncolumns)))
max_d = 0
for a in range(0, ncolumns):
y = self.mHeaderHeight + self.mDataHeight
for b in range(a * l, min(len(group_ids), (a + 1) * l)):
group_id = group_ids[b]
e = self.plotGene(x, y, group_id=group_id)
self.addElement(e)
t = str(group_id)
max_d = max(len(t) * self.mLegendFontSize * self.mFontFactor, max_d)
e = SVGdraw.text(
x + self.mBlockSize + self.mLegendVerticalSeparator,
y,
str(group_id),
self.mLegendFontSize,
self.mLegendFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="left",
)
self.addElement(e)
y += self.mLegendFontSize + self.mLegendHorizontalSeparator
x += max_d + 2 * self.mBlockSize + 2 * self.mLegendVerticalSeparator
def writeColLabels(self):
"""write column headers."""
y = self.mHeaderHeight
for contig in self.mSortedContigs1:
if contig not in self.mMapContig2Start1: continue
x = self.mHeaderWidth + self.mMapContig2Start1[contig]
e = SVGdraw.text(x,
y,
contig,
self.mLabelFontSize * self.mFontSizeFactor,
self.mLabelFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
self.addElement(e)
def writeColLabels( self ):
"""write column headers."""
y = self.mHeaderHeight
for contig in self.mSortedContigs1:
if contig not in self.mMapContig2Start1: continue
x = self.mHeaderWidth + self.mMapContig2Start1[contig]
e = SVGdraw.text( x,
y,
contig,
self.mLabelFontSize * self.mFontSizeFactor,
self.mLabelFont,
stroke = "rgb(%i,%i,%i)" % BLACK,
text_anchor = "start" )
self.addElement( e )
def writeColHeaders(self):
"""write row headers."""
current_x = self.mColWidth / 2
current_y = self.mHeaderHeight
i = 0
for name in self.mColNames:
e = SVGdraw.text(current_x,
current_y,
name,
self.mHeaderFontSize,
self.mHeaderFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start",
transform="rotate(-45,%i,%i)" % (current_x, current_y))
self.addElement(e)
current_x += self.mColWidth
def writeColHeaders( self ):
"""write row headers."""
current_x = self.mColWidth / 2
current_y = self.mHeaderHeight
i = 0
for name in self.mColNames:
e = SVGdraw.text( current_x,
current_y,
name,
self.mHeaderFontSize,
self.mHeaderFont,
stroke = "rgb(%i,%i,%i)" % BLACK,
text_anchor = "start",
transform="rotate(-45,%i,%i)" %( current_x, current_y ))
self.addElement(e)
current_x += self.mColWidth
def writeFooter(self):
"""write footer."""
current_x = self.mFooterX
current_y = self.mFooterY
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."""
current_x = self.mFooterX
current_y = self.mFooterY
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 writeRowLabels(self):
"""write column headers."""
x = self.mHeaderWidth
for contig in self.mSortedContigs2:
if contig not in self.mMapContig2Start2: continue
y = self.mHeaderHeight + self.mMapContig2Start2[
contig] + self.mMapContig2Size2[contig]
e = SVGdraw.text(x,
y,
contig,
self.mLabelFontSize * self.mFontSizeFactor,
self.mLabelFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start",
transform="rotate(-90,%i,%i)" % (x, y))
self.addElement(e)
def writeRowHeaders(self):
"""write row headers."""
current_x = self.mDataWidth + self.mSeparator
current_y = self.mHeaderHeight + self.mSeparator + self.mHeaderFontSize
for name in self.mRowNames:
e = SVGdraw.text(current_x,
current_y,
name,
self.mHeaderFontSize,
self.mHeaderFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="start")
self.addElement(e)
current_y += self.mRowHeight
self.mHeaderWidth = max(map(len,
self.mRowNames)) * self.mHeaderFontSize / 2