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 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 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 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 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 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 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 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 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 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, 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 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 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 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 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 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 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 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 getElements(self, node_id, x1, x2, y):
e = BranchDecoratorHorizontal.getElements(self, node_id, x1, x2, y)
text = self.getText(node_id)
d = x2 - x1
df = len(text) * (self.mFontSize / 2)
if df > d:
x = x1 - df
else:
x = x1 + (x2 - x1 - df) / 2
e.append(SVGdraw.text(x, y - 5,
text,
self.mFontSize,
self.mFont,
stroke="rgb(%i,%i,%i)" % self.mFontColour,
text_anchor="left"))
return 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
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
def getElements(self, node_id, x1, x2, y):
e = BranchDecoratorHorizontal.getElements(self, node_id, x1, x2, y)
text = self.getText(node_id)
d = x2 - x1
df = len(text) * (self.mFontSize / 2)
if df > d:
x = x1 - df
else:
x = x1 + (x2 - x1 - df) / 2
e.append(
SVGdraw.text(x,
y - 5,
text,
self.mFontSize,
self.mFont,
stroke="rgb(%i,%i,%i)" % self.mFontColour,
text_anchor="left"))
return e
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 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 getElements(self, x, y, map_node2height):
t = self.mTree.get_terminals()
elements = []
# print locations
if self.mPrintLocation:
for i in range(len(t)):
node_id1 = t[i]
taxon1 = self.mTree.node(node_id1).data.taxon
y1 = map_node2height[node_id1] + y
elements.append(SVGdraw.text(x, y1,
str(self.mMapId2Location[
taxon1]),
self.mFontSize,
self.mFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="left"))
# print connectors
for i in range(len(t) - 1):
node_id1 = t[i]
taxon1 = self.mTree.node(node_id1).data.taxon
y1 = map_node2height[node_id1] + y
for j in range(i + 1, len(t)):
node_id2 = t[j]
taxon2 = self.mTree.node(node_id2).data.taxon
if self.mExtractSpecies:
species1 = self.mExtractSpecies(taxon1)
species2 = self.mExtractSpecies(taxon2)
if species1 != species2:
continue
if species1 not in self.mMapSpecies2Colour:
self.mMapSpecies2Colour[species1] = COLOURS[
len(self.mMapSpecies2Colour) % len(COLOURS)]
colour = self.mMapSpecies2Colour[species1]
else:
colour = self.mDefaultColour
l1 = self.mMapId2Location[taxon1]
l2 = self.mMapId2Location[taxon2]
if l1.contig != l2.contig:
continue
if self.mMaxSeparation:
s = min(abs(l1.mFrom - l2.mTo), abs(l1.mTo - l2.mFrom))
if s >= self.mMaxSeparation:
continue
y2 = map_node2height[node_id2] + y
distance = y2 - y1
d = SVGdraw.pathdata(x, y1)
d.line(x + self.mTickWidth, y1)
d.ellarc(distance, distance, 0, 0, 1, x + self.mTickWidth, y2)
d.line(x, y2)
e = SVGdraw.path(d,
fill="none",
stroke="rgb(%i,%i,%i)" % colour,
stroke_width=1)
elements.append(e)
return elements
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.
"""
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 getElements(self, x, y, map_node2height):
t = self.mTree.get_terminals()
elements = []
# print locations
if self.mPrintLocation:
for i in range(len(t)):
node_id1 = t[i]
taxon1 = self.mTree.node(node_id1).data.taxon
y1 = map_node2height[node_id1] + y
elements.append(
SVGdraw.text(x,
y1,
str(self.mMapId2Location[taxon1]),
self.mFontSize,
self.mFont,
stroke="rgb(%i,%i,%i)" % BLACK,
text_anchor="left"))
# print connectors
for i in range(len(t) - 1):
node_id1 = t[i]
taxon1 = self.mTree.node(node_id1).data.taxon
y1 = map_node2height[node_id1] + y
for j in range(i + 1, len(t)):
node_id2 = t[j]
taxon2 = self.mTree.node(node_id2).data.taxon
if self.mExtractSpecies:
species1 = self.mExtractSpecies(taxon1)
species2 = self.mExtractSpecies(taxon2)
if species1 != species2:
continue
if species1 not in self.mMapSpecies2Colour:
self.mMapSpecies2Colour[species1] = COLOURS[len(
self.mMapSpecies2Colour) % len(COLOURS)]
colour = self.mMapSpecies2Colour[species1]
else:
colour = self.mDefaultColour
l1 = self.mMapId2Location[taxon1]
l2 = self.mMapId2Location[taxon2]
if l1.contig != l2.contig:
continue
if self.mMaxSeparation:
s = min(abs(l1.mFrom - l2.mTo), abs(l1.mTo - l2.mFrom))
if s >= self.mMaxSeparation:
continue
y2 = map_node2height[node_id2] + y
distance = y2 - y1
d = SVGdraw.pathdata(x, y1)
d.line(x + self.mTickWidth, y1)
d.ellarc(distance, distance, 0, 0, 1, x + self.mTickWidth, y2)
d.line(x, y2)
e = SVGdraw.path(d,
fill="none",
stroke="rgb(%i,%i,%i)" % colour,
stroke_width=1)
elements.append(e)
return elements
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)
