def addChromosomes(drawing, chrNames, chrSizes, xmap, ymap, w=0.1*DPI, fillColor=colors.skyblue, strokeColor=colors.skyblue):
for i,chrom in enumerate(chrNames):
x = xmap(i+1)
y = ymap(chrSizes[chrom])
h = ymap(1)-ymap(chrSizes[chrom])
chromosome = Rect(x,y,w,h, strokeColor=strokeColor, fillColor=fillColor)
drawing.add(chromosome)
topCap = Wedge(x+0.5*w, y+h, 0.5*w, 0, 180, strokeColor=strokeColor, fillColor=fillColor)
bottomCap = Wedge(x+0.5*w, y, 0.5*w, 180, 0, strokeColor=strokeColor, fillColor=fillColor)
drawing.add(topCap)
drawing.add(bottomCap)
label = Label()
label.setOrigin(xmap(i+1)+w/2, ymap(0))
label.boxAnchor = 's'
label.textAnchor = 'middle'
label.dx = 0
label.dy = DPI/10
label.setText(chrom)
label.fontSize = 36
label.fontName = 'Helvetica'
drawing.add(label)
chrLength = Label()
chrLength.setOrigin(xmap(i+1)+w/2, ymap(chrSizes[chrom]))
chrLength.boxAnchor = 'n'
chrLength.textAnchor = 'middle'
chrLength.dx = 0
chrLength.dy = -DPI/10
chrLength.setText('%iMb' % int(chrSizes[chrom]/1e6))
chrLength.fontSize = 24
chrLength.fontName = 'Helvetica'
drawing.add(chrLength)
def _drawLabels(self, Title, xAxis, yAxis):
self.graphCenterX = self.width/2
self.graphCenterY = self.height/2
Label_Xaxis = Label()
Label_Xaxis.fontSize = 7
Label_Xaxis.angle = 0
Label_Xaxis.dx = self.graphCenterX - 50
Label_Xaxis.dy = 0
Label_Xaxis.boxAnchor = 's'
Label_Xaxis.setText(xAxis)
self.drawing.add(Label_Xaxis)
Label_Yaxis = Label()
Label_Yaxis.fontSize = 7
Label_Yaxis.angle = 90
Label_Yaxis.boxAnchor = 'n'
Label_Yaxis.dx = -5
Label_Yaxis.dy = self.graphCenterY
Label_Yaxis.setText(yAxis)
self.drawing.add(Label_Yaxis)
Label_Graph = Label()
Label_Graph.fontSize = 10
Label_Graph.angle = 0
Label_Graph.boxAnchor = 'n'
Label_Graph.dx = self.graphCenterX - 50
Label_Graph.dy = self.height
Label_Graph.setText(Title)
self.drawing.add(Label_Graph)
def addChromosomes(drawing,
chrNames,
chrSizes,
xmap,
ymap,
w=0.1 * DPI,
fillColor=colors.skyblue,
strokeColor=colors.skyblue):
for i, chrom in enumerate(chrNames):
x = xmap(i + 1)
y = ymap(chrSizes[chrom])
h = ymap(1) - ymap(chrSizes[chrom])
chromosome = Rect(x,
y,
w,
h,
strokeColor=strokeColor,
fillColor=fillColor)
drawing.add(chromosome)
topCap = Wedge(x + 0.5 * w,
y + h,
0.5 * w,
0,
180,
strokeColor=strokeColor,
fillColor=fillColor)
bottomCap = Wedge(x + 0.5 * w,
y,
0.5 * w,
180,
0,
strokeColor=strokeColor,
fillColor=fillColor)
drawing.add(topCap)
drawing.add(bottomCap)
label = Label()
label.setOrigin(xmap(i + 1) + w / 2, ymap(0))
label.boxAnchor = 's'
label.textAnchor = 'middle'
label.dx = 0
label.dy = DPI / 10
label.setText(chrom)
label.fontSize = 36
label.fontName = 'Helvetica'
drawing.add(label)
chrLength = Label()
chrLength.setOrigin(xmap(i + 1) + w / 2, ymap(chrSizes[chrom]))
chrLength.boxAnchor = 'n'
chrLength.textAnchor = 'middle'
chrLength.dx = 0
chrLength.dy = -DPI / 10
chrLength.setText('%iMb' % int(chrSizes[chrom] / 1e6))
chrLength.fontSize = 24
chrLength.fontName = 'Helvetica'
drawing.add(chrLength)
def getTalkRect(self, startTime, duration, trackId, text):
"Return shapes for a specific talk"
g = Group()
y_bottom = self.scaleTime(startTime + duration)
y_top = self.scaleTime(startTime)
y_height = y_top - y_bottom
if trackId is None:
#spans all columns
x = self._colLeftEdges[1]
width = self.width - self._colWidths[0]
else:
#trackId is 1-based and these arrays have the margin info in column
#zero, so no need to add 1
x = self._colLeftEdges[trackId]
width = self._colWidths[trackId]
lab = Label()
lab.setText(text)
lab.setOrigin(x + 0.5*width, y_bottom+0.5*y_height)
lab.boxAnchor = 'c'
lab.width = width
lab.height = y_height
lab.fontSize = 6
r = Rect(x, y_bottom, width, y_height, fillColor=colors.cyan)
g.add(r)
g.add(lab)
#now for a label
# would expect to color-code and add text
return g
def addScale(drawing, xmap, y, start, end, tickLen=10, dx=3, dy=6,
textAnchor='middle', boxAnchor='s', fontSize=12,
strokeWidth=1, strokeColor=colors.black, scale=1.0, format='%ibp'):
x1 = xmap(start)
x2 = xmap(end)
line = Line(x1+dx,y,x2-dx,y,
strokeWidth=strokeWidth, strokeColor=strokeColor)
drawing.add(line)
leftTick = Line(x1+dx,y-0.5*tickLen,x1+dx,y+0.5*tickLen,
strokeWidth=strokeWidth, strokeColor=strokeColor)
drawing.add(leftTick)
rightTick = Line(x2-dx,y-0.5*tickLen,x2-dx,y+0.5*tickLen,
strokeWidth=strokeWidth, strokeColor=strokeColor)
drawing.add(rightTick)
label = Label()
label.setOrigin(0.5*(x1+x2), y+dy)
distance = float(end-start)/scale
label.setText(format % (distance/scale))
label.fontSize = fontSize
label.textAnchor = textAnchor
label.boxAnchor = boxAnchor
drawing.add(label)
def _drawLabels(self, label, labelCenter, y, width):
"""
Draw the label given in a given area originating at (x,y) with width 'width'
"""
fontName = 'Times-Roman'
fontSize = 10
#Limit the length of the label to the boundaries of the chartAreaWidth
strWidth = self._stringWidth(label, fontName, fontSize)
#Calculate the area taken by one character
oneCharWidth = self._stringWidth(label[0], fontName, fontSize)
#If the given string needs more size, reduce the string to a length which fits
#in the given area
if strWidth > width:
maxPossibleLen = int(width/oneCharWidth)
label = label[:maxPossibleLen]
strWidth = self._stringWidth(label, fontName, fontSize)
x = (labelCenter - ((strWidth)/2))
Label_Graph = Label()
Label_Graph.fontName = fontName
Label_Graph.fontSize = fontSize
#Label_Graph.angle = 0
Label_Graph.boxAnchor = 'n'
Label_Graph.x = x
Label_Graph.y = y
Label_Graph.setText(label)
self.drawing.add(Label_Graph)
def draw(self):
# general widget bits
w = float(self.length)
h = float(self.height)
g = shapes.Group()
body = shapes.Polygon(
[self.x-0.5*w, self.y-0.5*w,
self.x-0.5*w, self.y+0.5*w,
self.x+0.5*w, self.y],
fillColor=self.fillColor,
strokeColor=self.strokeColor,
strokeWidth=self.strokeWidth)
g.add(body)
if self.label:
b = g.getBounds()
s = Label()
s.setText(self.label)
s.setOrigin(self.x+0.5*w, self.y-h/2+b[3]-b[1]+4)
s.boxAnchor = self.boxAnchor
s.textAnchor = self.textAnchor
s.fontName = 'Helvetica'
s.fontSize = self.fontSize
s.angle = self.labelAngle
g.add(s)
return g
def graphout_stackedBar(data, labels, X, Y):
drawing = Drawing(X*inch, Y*inch)
bar = VerticalBarChart()
bar.x = 50
bar.y = 50
bar.width = (X-2)*inch
bar.height = (Y-1)*inch
bar.data = data
bar.bars.strokeWidth = 0
bar.categoryAxis.style='stacked'
bar.categoryAxis.labels.boxAnchor = 'ne'
bar.categoryAxis.labels.dx = -2
bar.categoryAxis.labels.dy = -2
bar.categoryAxis.labels.angle = 45
bar.categoryAxis.categoryNames = labels
# ensure bar chart and legend coloring matches
for i in range(len(data)):
bar.bars[i].fillColor = colorList[i]
# Create a title for the y-axis
yLabel = Label()
yLabel.setOrigin(0, 50) # for reference, the graph origin is (50, 50)
yLabel.boxAnchor = 'c'
yLabel.angle = 90
yLabel.setText('Data Storage [GB]')
yLabel.fontSize=16
yLabel.dy = 1.25*inch
drawing.add(yLabel)
drawing.add(bar)
return drawing
def getTalkRect(self, startTime, duration, trackId, text):
"Return shapes for a specific talk"
g = Group()
y_bottom = self.scaleTime(startTime + duration)
y_top = self.scaleTime(startTime)
y_height = y_top - y_bottom
if trackId is None:
#spans all columns
x = self._colLeftEdges[1]
width = self.width - self._colWidths[0]
else:
#trackId is 1-based and these arrays have the margin info in column
#zero, so no need to add 1
x = self._colLeftEdges[trackId]
width = self._colWidths[trackId]
lab = Label()
lab.setText(text)
lab.setOrigin(x + 0.5 * width, y_bottom + 0.5 * y_height)
lab.boxAnchor = 'c'
lab.width = width
lab.height = y_height
lab.fontSize = 6
r = Rect(x, y_bottom, width, y_height, fillColor=colors.cyan)
g.add(r)
g.add(lab)
#now for a label
# would expect to color-code and add text
return g
def write_label(label, width, height, person):
text = "\n".join((person['name'], person['addresses'][0]))
lab = Label()
lab.setOrigin(8, height - 5)
lab.fontSize = 14
lab.setText(text)
lab.boxAnchor = 'nw'
label.add(lab)
def draw(self):
# general widget bits
w = float(self.length)
h = float(self.height)
# print self.label,w,h
# Set minimum size
if abs(w)<self.wmin:
xmid = self.x+0.5*w
w = w/abs(w) * self.wmin
self.x = xmid-0.5*w
g = shapes.Group()
if abs(w)>self.wNoTail:
# arrow specific bits
body = shapes.Rect(x=self.x, y=self.y-self.aspectRatio*h/2,
width=2*(w/3),
height=self.aspectRatio*h,
fillColor=self.fillColor,
strokeColor=self.strokeColor,
strokeWidth=self.strokeWidth)
g.add(body)
head = shapes.Polygon(
points=[self.x+w, self.y,
self.x+2*(w/3), self.y+h/2,
self.x+2*(w/3), self.y-h/2,
self.x+w, self.y],
fillColor=self.fillColor,
strokeColor=self.strokeColor,
strokeWidth=self.strokeWidth)
g.add(head)
else:
head = shapes.Polygon(
points=[self.x+w, self.y,
self.x, self.y+h/2,
self.x, self.y-h/2,
self.x+w, self.y],
fillColor=self.fillColor,
strokeColor=self.strokeColor,
strokeWidth=self.strokeWidth)
g.add(head)
if self.label:
b = g.getBounds()
s = Label()
s.setText(self.label)
s.setOrigin(self.x+0.5*w+self.labeldx, self.y-h/2+b[3]-b[1]+self.labeldy)
s.boxAnchor = self.boxAnchor
s.textAnchor = self.textAnchor
s.fontName = 'Helvetica'
s.fontSize = self.fontSize
s.angle = self.labelAngle
g.add(s)
return g
def addLabel(drawing, x, y, text, fontName='Helvetica', fontSize=11, dy=0,
angle=0, boxAnchor='sw', textAnchor='start'):
"""Add a label to the drawing.
This interface here is inconsistent in that it requires pixel coords. FIX
This just sets convenient defaults for Label."""
label = Label()
label.setText(text)
label.setOrigin(x, y)
label.fontName = fontName
label.fontSize = fontSize
label.boxAnchor = boxAnchor
label.textAnchor = textAnchor
label.dy = dy
label.angle = angle
drawing.add(label)
def addPointyCompoundFeature(drawing, xmap, y, gene,
strokeColor=None, fillColor=colors.blue, intronColor=colors.blue,
glyph=PointyBlock, height=12, utrHeight=6, rise=8,
labeldy=10, fontSize=10, textAnchor='middle', boxAnchor='s'):
"""Adds a pointy compound feature to the drawing. This is typically
several exons joined by zig-zag lines with an arrow showing strand."""
if gene.strand=='+':
x1,x2 = xmap(gene.start), xmap(gene.end)
else:
x2,x1 = xmap(gene.start), xmap(gene.end)
y = y+height/2
y1 = y
line = Line(x1,y1,x2,y1,strokeColor=intronColor)
drawing.add(line)
for exon in gene:
if exon.strand=='+':
x1,x2 = xmap(exon.start), xmap(exon.end)
else:
x2,x1 = xmap(exon.start), xmap(exon.end)
g = glyph()
g.x = x1
g.y = y
if exon.kind.lower()=='utr':
g.height = utrHeight
else:
g.height = height
g.length = x2-x1
g.fillColor = fillColor
if strokeColor:
g.strokeColor = strokeColor
else:
g.strokeColor = fillColor
g.fontSize = fontSize
drawing.add(g)
label = Label()
label.setText(gene.name)
x = 0.5*(gene.start+gene.end)
label.setOrigin(x,y)
label.dy = labeldy
label.textAnchor = textAnchor
label.boxAnchor = boxAnchor
drawing.add(label)
def addAxis(drawing, xmap, y, strokeWidth=1, minorStrokeWidth=0.5,
tickDir='down', autoTicks=False, nTicks=20, tickLen=5, fontSize=10, nMinorTicks=80,
minorTickLen=2, angle=0, dx=0, dy=-2, textAnchor='middle', boxAnchor=None,
scale=1.0, format='%i'):
"""Add a horizontal axis to the drawing.
To do: Round tick positions
"""
line = Line(xmap.x0, y, xmap.x1, y, strokeWidth=strokeWidth)
drawing.add(line)
if not boxAnchor:
if tickDir=='down':
boxAnchor = 'n'
else:
boxAnchor = 's'
signum = {'up': -1, 'down': 1}[tickDir]
if nTicks>0:
ticks = tick_generator(xmap.start, xmap.end, n=nTicks, convert=int)
for p in ticks:
x = xmap(p)
line = Line(x, y, x, y-signum*tickLen, strokeWidth=strokeWidth)
drawing.add(line)
s = Label()
s.setOrigin(x, y-signum*tickLen)
s.setText(format % (p/scale))
s.dx = dx
s.dy = signum*dy
s.fontName = 'Helvetica'
s.fontSize = fontSize
s.textAnchor = textAnchor
s.boxAnchor = boxAnchor
s.angle = angle
drawing.add(s)
minorticks = tick_generator(xmap.start, xmap.end, n=nMinorTicks, convert=int)
for p in minorticks:
x = xmap(p)
line = Line(x, y, x, y-signum*minorTickLen, strokeWidth=minorStrokeWidth)
drawing.add(line)
def simple_label():
drawing = shapes.Drawing(width=400, height=200)
drawing.add(shapes.Rect(200, 100, 10, 10, fillColor=colors.red))
x = 50
angle = 0
for item in range(3):
label = Label()
label.setOrigin(200, 100)
label.boxAnchor = 'se'
label.angle = angle
#label.boxStrokeColor = colors.black
label.setText('ReportLab label')
drawing.add(label)
x += 25
angle += 45
renderPDF.drawToFile(drawing, 'simple_label.pdf')
def border():
draw = Drawing(1, 1)
rect = Polygon(points=[
-12, cm / 6, (PAGE_WIDTH - (RIGHT_MARGIN + LEFT_MARGIN)), cm / 6,
PAGE_WIDTH - (RIGHT_MARGIN + LEFT_MARGIN),
-1 * (PAGE_HEIGHT - (TOP_MARGIN + BOTTOM_MARGIN + cm / 2)), -12,
-1 * (PAGE_HEIGHT - (TOP_MARGIN + BOTTOM_MARGIN + cm / 2))
],
strokeColor=Color(*charts.BG_COLOR))
rect.fillColor = Color(*charts.BG_COLOR, 0.1)
draw.add(rect)
draw.add(Circle(100, 90, 5, fillColor=colors.green))
lab = Label()
lab.setOrigin(350, -50)
lab.boxAnchor = 'ne'
lab.fillColor = Color(*charts.BG_COLOR, 0.15)
lab.fontSize = 72
lab.angle = 60
lab.dx = 0
lab.dy = 0
lab.setText('Wisdom Tests')
draw.add(lab)
return draw
def addAxis(drawing, xmap, y, fontSize=8, tickLen=4, minorTickLen=2,
nTicks=20, strokeWidth=1, minorStrokeWidth=0.5):
line = Line(xmap.x0, y, xmap.x1, y, strokeWidth=strokeWidth)
drawing.add(line)
ticks = tick_generator(xmap.start, xmap.end, n=nTicks, convert=int)
for p in ticks:
x = xmap(p)
line = Line(x, y, x, y-tickLen, strokeWidth=strokeWidth)
drawing.add(line)
s = Label()
s.setOrigin(x, y-tickLen)
s.setText(str(p))
s.fontName = 'Helvetica'
s.fontSize = fontSize
s.textAnchor = 'middle'
s.boxAnchor = 'n'
drawing.add(s)
minorticks = tick_generator(xmap.start, xmap.end, n=50, convert=int)
for p in minorticks:
x = xmap(p)
line = Line(x, y, x, y-minorTickLen, strokeWidth=minorStrokeWidth)
drawing.add(line)
def exportMonthlyReport(self, file, month, year):
"""Outputs the monthly report to the specified file location
Parameters:
self: the class instance
file: str - file location and name ending in .pdf
month: str - required month
year: int - required year
"""
# For conversion of month to three letter abbreviation
months = [
'Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep',
'Oct', 'Nov', 'Dec'
]
# Creating a title
title = Label()
title.setOrigin(300, 20)
title.boxAnchor = 'ne'
title.dx = 0
title.dy = -5
title.fontSize = 30
title.setText("Monthly Report")
# Adding title to a drawing
draw_title = Drawing(0, 40)
draw_title.add(title)
# Creating a subtitle
subtitle = Label()
subtitle.setOrigin(320, 20)
subtitle.boxAnchor = 'ne'
subtitle.dx = 0
subtitle.dy = -10
subtitle.fontSize = 14
# Converts month to three letter abbreviation
str_month = months[int(month) - 1]
# Setting the subtitle's text
subtitle.setText("Australia Zoo Wildlife Hospital, " + str_month +
" " + str(year))
# Adding subtitle to a drawing
draw_subtitle = Drawing(0, 30)
draw_subtitle.add(subtitle)
# Creating a label for the first chart
label_lga = Label()
label_lga.setOrigin(180, 20)
label_lga.boxAnchor = 'ne'
label_lga.dx = 0
label_lga.dy = -20
label_lga.setText("Local Government Area Totals")
# Adding label to a drawing
draw_label_lga = Drawing(0, 40)
draw_label_lga.add(label_lga)
# Creating drawing for the lga chart
draw_lga = Drawing(0, 270)
draw_lga.add(self.getSpecificBarChart("LGA", month, year))
# Creating a label for the second chart
label_taxons = Label()
label_taxons.setOrigin(180, 20)
label_taxons.boxAnchor = 'ne'
label_taxons.dx = 0
label_taxons.dy = -20
label_taxons.setText("Taxon Grouping Totals")
# Adding label to a drawing
draw_label_taxons = Drawing(0, 40)
draw_label_taxons.add(label_taxons)
# Creating drawing for the taxons chart
draw_taxons = Drawing(0, 270)
draw_taxons.add(self.getSpecificBarChart("Taxons", month, year))
# List of drawings in order of how to place them in the canvas
drawlist = [
draw_title, draw_subtitle, draw_label_lga, draw_lga,
draw_label_taxons, draw_taxons
]
# Creating a canvas (pdf file) and saving it to a location
canvas = Canvas(file)
# Creating a frame to add flowables (drawings) to
frame = Frame(inch, 0, 15.92 * cm, 29.7 * cm)
# Adding flowables
frame.addFromList(drawlist, canvas)
# Saving the pdf
canvas.save()
legend.fontName = 'Helvetica'
legend.fontSize = 8
legend.dxTextSpace = 5
legend.dy = 5
legend.dx = 5
legend.deltay = 5
legend.alignment ='right'
drawing.add(lp)
drawing.add(legend)
if title != None:
label = Label()
label.x = w
label.y = h - 25
label.boxAnchor = 'se'
label.fontName = 'Helvetica'
label.fontSize = 10
label.setText(title)
drawing.add(label)
return drawing
def drawTable(self, data):
t = Table(data, None, None, None, 1, 1, 1)
extraStyle = []
for i in range(len(data[1:])):
if data[1:][i][0] == 'Free' or data[1:][i][0] == 'Used':
extraStyle.append(('BACKGROUND', (0, i + 1), (-1, i + 1), colors.orange))
if data[1:][i][0] == 'SwapUsage' or data[1:][i][0] == 'LMK File':
extraStyle.append(('BACKGROUND', (0, i + 1), (-1, i + 1), colors.lightgreen))
t.setStyle(TableStyle([('FONT', (0, 0), (-1, -1), 'Helvetica'),
def _rawDraw(self, x, y):
from reportlab.lib import colors
from reportlab.graphics.shapes import Drawing, Line, String, STATE_DEFAULTS
from reportlab.graphics.charts.axes import XCategoryAxis,YValueAxis
from reportlab.graphics.charts.textlabels import Label
from reportlab.graphics.charts.barcharts import VerticalBarChart
self.originX = x
self.originY = y
self._setScale([self.dataBar])
(x1, y1, Width, Height) = self._getGraphRegion(x, y)
#Build the graph
self.drawing = Drawing(self.width, self.height)
#Size of the Axis
SizeXaxis = 14
countSteps = int(self.valueMax / self.valueStep)
SizeYaxis = 0.0
for n in range(countSteps + 1):
eachValue = self.valueMin + n * self.valueStep
textString = self._customSecondsLabelFormat( eachValue )
SizeYaxis = max(SizeYaxis, self._stringWidth(textString, STATE_DEFAULTS['fontName'], STATE_DEFAULTS['fontSize']) )
bc = VerticalBarChart()
SizeYaxis += bc.valueAxis.tickLeft
bc.x = x1 - x + SizeYaxis
bc.y = y1 - y + SizeXaxis
bc.height = Height - SizeXaxis
bc.width = Width - SizeYaxis
self.graphCenterX = bc.x + bc.width/2
self.graphCenterY = bc.y + bc.height/2
if self.validData:
# add valid data to chart
bc.data = self.dataBar
bc.categoryAxis.categoryNames = self.dataNames
# axis values
bc.valueAxis.valueMin = self.valueMin
bc.valueAxis.valueMax = self.valueMax
bc.valueAxis.valueStep = self.valueStep
# add value labels above bars
bc.barLabelFormat = self._customSecondsLabelFormat
bc.barLabels.dy = 0.08*inch
bc.barLabels.fontSize = 6
else:
# no valid data
bc.data = [ (0, ), ]
bc.categoryAxis.categoryNames = [ '' ]
bc.valueAxis.valueMin = 0
bc.valueAxis.valueMax = 1
bc.valueAxis.valueStep = 1
Nodata = Label()
Nodata.fontSize = 12
Nodata.angle = 0
Nodata.boxAnchor = 'c'
Nodata.dx = self.graphCenterX
Nodata.dy = self.graphCenterY
Nodata.setText("NO VALID DATA")
self.drawing.add(Nodata)
# chart formatting
(R,G,B) = VeriwaveYellow
bc.bars[0].fillColor = colors.Color(R,G,B)
bc.valueAxis.labelTextFormat = self._customSecondsLabelFormat
# axis labels
bc.categoryAxis.labels.boxAnchor = 'c'
bc.categoryAxis.labels.dx = 0
bc.categoryAxis.labels.dy = -10
bc.categoryAxis.labels.angle = 0
bc.categoryAxis.labels.fontSize = 8
# add chart
self.drawing.add(bc)
#Adjust the labels to be the center of the graph
self._drawLabels(self.title, "", "")
# Add Legend in upper right corner
legendHeight = 9
legendX = bc.x + 5
legendY = bc.y + bc.height - 12
self.drawing.add(Line(legendX, legendY + 3 , legendX + 20, legendY + 3, strokeColor=bc.bars[0].fillColor, strokeWidth=3 ))
self.drawing.add(String(legendX + 22, legendY, 'MIN', fontName='Helvetica', fontSize=8))
legendY -= legendHeight
self.drawing.add(Line(legendX, legendY + 3 , legendX + 20, legendY + 3, strokeColor=bc.bars[1].fillColor, strokeWidth=3 ))
self.drawing.add(String(legendX + 22, legendY, 'MAX', fontName='Helvetica', fontSize=8))
legendY -= legendHeight
self.drawing.add(Line(legendX, legendY + 3 , legendX + 20, legendY + 3, strokeColor=bc.bars[2].fillColor, strokeWidth=3 ))
self.drawing.add(String(legendX + 22, legendY, 'AVG', fontName='Helvetica', fontSize=8))
legendY -= legendHeight
def create_bar(self,
data_list,
label_x_axis,
contain,
y_label=None,
x_label=None,
bar_width=520,
bar_height=100,
draw_width=520,
draw_height=200,
user_color=None,
fontName="Times-Roman",
fontSize=6,
x_angle=0,
bar_space=0):
d = Drawing(width=draw_width, height=draw_height)
bar = VerticalBarChart()
bar.width = bar_width
bar.height = bar_height
bar.y = bar.height - (bar_height / 4)
bar.strokeColor = colors.black
bar.barLabelFormat = '%s'
bar.barLabels.nudge = 7
bar.barLabels.fontSize = fontSize
################# X AXIS PROPERTIES #################
bar.categoryAxis.labels.dx = 0
bar.categoryAxis.labels.angle = x_angle
bar.categoryAxis.labels.boxAnchor = 'autox'
bar.categoryAxis.labels.fontSize = fontSize
bar.categoryAxis.labels.fontName = self.master_font
bar.categoryAxis.strokeWidth = 0.25
bar.categoryAxis.tickDown = -(bar.height)
bar.categoryAxis.categoryNames = label_x_axis
labX = Label()
labX.boxAnchor = 'ne'
labX.dx = bar.width * 2.15
labX.dy = bar.height
labX.fontName = fontName
labX.fontSize = fontSize
labX.setText(x_label)
d.add(labX)
#####################################################
################# Y AXIS PROPERTIES #################
bar.valueAxis.forceZero = 1
bar.valueAxis.labels.fontSize = fontSize
bar.valueAxis.labels.fontName = fontName
bar.valueAxis.rangeRound = 'both'
bar.valueAxis.valueMin = 0
bar.valueAxis.visibleGrid = 1
bar.valueAxis.visibleAxis = 1
bar.valueAxis.labels.dx = -10
labY = Label()
labY.boxAnchor = 'autox'
labY.dy = bar.y + (bar.height / 1.5)
labY.dx = bar.x - 30
labY.angle = 90
labY.fontName = fontName
labY.fontSize = fontSize
labY.setText(y_label)
d.add(labY)
#####################################################
bar.barSpacing = bar_space
# bar.groupSpacing = 3
bar.data = data_list
# print len(data_list)
# print len(contain)
if user_color != None:
usage_color = user_color
else:
random_range = [randint(0, 100) for i in range(len(contain))]
usage_color = map(
lambda item: PCMYKColor(randint(0, item), randint(0, item),
randint(0, item), randint(0, item)),
random_range)
for i in range(len(data_list)):
bar.bars[i].name = contain[i].upper()
bar.bars[i].fillColor = usage_color[i]
legend = Legend()
# legend.autoXPadding = 10
legend.alignment = 'right'
legend.boxAnchor = 'sw'
legend.dxTextSpace = 10
legend.fontSize = fontSize
legend.fontName = fontName
legend.subCols.minWidth = 55
legend.variColumn = 1
legend.deltay = 15
legend.x = bar.x
legend.colorNamePairs = Auto(obj=bar)
d.add(bar)
d.add(legend)
self.flowables.append(d)
d.add(lab)
"""
)
from reportlab.graphics import shapes
from reportlab.graphics.charts.textlabels import Label
d = Drawing(200, 100)
# mark the origin of the label
d.add(Circle(100, 90, 5, fillColor=colors.green))
lab = Label()
lab.setOrigin(100, 90)
lab.boxAnchor = "ne"
lab.angle = 45
lab.dx = 0
lab.dy = -20
lab.boxStrokeColor = colors.green
lab.setText("Some\nMulti-Line\nLabel")
d.add(lab)
draw(d, "Label example")
disc(
"""
In the drawing above, the label is defined relative to the green blob.
The text box should have its north-east corner ten points down from
def balance_statistics_chart(self, control_vars, match_vars, var_names):
"""
Specify layout of the balance statistics chart and generate
flowable object that can be added to the pdf
"""
drawing = Drawing()
vbc = VerticalBarChart()
# Chart position in document
vbc.x = self.chart_offset_x
vbc.y = self.chart_offset_y
vbc.height = self.chart_height
vbc.width = self.chart_width
# Specify data
# [[control_var1, control_var2], [match_var1, match_var2]]
vbc.data = [control_vars, match_vars]
#Set Y-Axis ranges
#axis_range = self._calculate_y_axis(vbc.data)
#vbc.valueAxis.valueMin = axis_range['min']
#vbc.valueAxis.valueMax = axis_range['max']
#vbc.valueAxis.valueStep = axis_range['step']
#Grid formatting
vbc.valueAxis.visibleGrid = 1
vbc.valueAxis.gridStrokeColor = colors.lightgrey
#Bar formatting
vbc.bars[0].fillColor = colors.blue
vbc.bars[1].fillColor = colors.yellow
vbc.bars.strokeColor = None
vbc.groupSpacing = 1
vbc.barWidth = 5
# Callout label formatting (numbers above bar)
#vbc.barLabels.fontName = "Arial"
vbc.barLabels.fontSize = 8
vbc.barLabels.fillColor = colors.black
vbc.barLabelFormat = '%.2f'
vbc.barLabels.nudge = 5
# Central axis
vbc.categoryAxis.visibleTicks = 1
# X-axis labels
#vbc.categoryAxis.labels.dy = -60
vbc.valueAxis.labels.fontName = 'Helvetica'
vbc.categoryAxis.categoryNames = var_names
lab = Label()
lab.setOrigin(10, 155)
lab.boxAnchor = 'ne'
lab.angle = 90
lab.dx = 0
lab.dy = -15
#lab.boxStrokeColor = colors.green
lab.setText('Percent Bias')
drawing.add(lab)
drawing.add(vbc)
self.elements.append(drawing)
def results_chart(self, control_mean, match_mean, treated_mean, att):
"""
Specify layout of the results chart and generate
flowable object that can be added to the pdf
"""
drawing = Drawing()
vbc = VerticalBarChart()
# Offset chart from border and text
vbc.x = self.chart_offset_x
vbc.y = self.chart_offset_y
# Set figure size
vbc.height = self.chart_height
vbc.width = self.chart_width
# Specify chart -- list of lists -- list of series with enteries
vbc.data = [[control_mean, match_mean, treated_mean, att]]
#Set Y-Axis ranges
#axis_range = self._calculate_y_axis(vbc.data)
#vbc.valueAxis.valueMin = axis_range['min']
#vbc.valueAxis.valueMax = axis_range['max']
#vbc.valueAxis.valueStep = axis_range['step']
#Grid formatting
vbc.valueAxis.visibleGrid = 1
vbc.valueAxis.gridStrokeColor = colors.lightgrey
# Set bar characteristics
vbc.bars[(0, 0)].fillColor = colors.blue
vbc.bars[(0, 1)].fillColor = colors.yellow
vbc.bars[(0, 2)].fillColor = colors.red
vbc.bars[(0, 3)].fillColor = colors.green
vbc.bars.strokeColor = None
vbc.barSpacing = 2
# Create callout labels
#vbc.barLabels.fontName = "Helvetica"
vbc.barLabels.fontSize = 8
vbc.barLabels.fillColor = colors.black
vbc.barLabelFormat = '%.2f'
vbc.barLabels.nudge = 5
# X-axis labels
#vbc.categoryAxis.labels.dy = -60
#vbc.valueAxis.labels.fontName = 'Helvetica'
vbc.categoryAxis.categoryNames = [
'Control Mean', 'Matched Control Mean', 'Treatment mean', 'ATT'
]
lab = Label()
lab.setOrigin(10, 155)
lab.boxAnchor = 'ne'
lab.angle = 90
lab.dx = 0
lab.dy = -15
#lab.boxStrokeColor = colors.green
lab.setText('Result Values')
drawing.add(lab)
drawing.add(vbc)
self.elements.append(drawing)
def draw(self):
g = Group()
#box
g.add(
Rect(self.x,
self.y,
len(self.xlabels) * self.gridDivWidth,
len(self.ylabels) * self.gridDivWidth,
strokeColor=self.gridColor,
strokeWidth=self.strokeWidth,
fillColor=None))
#internal gridding
for f in range(1, len(self.ylabels)):
#horizontal
g.add(
Line(strokeColor=self.gridColor,
strokeWidth=self.strokeWidth,
x1=self.x,
y1=self.y + f * self.gridDivWidth,
x2=self.x + len(self.xlabels) * self.gridDivWidth,
y2=self.y + f * self.gridDivWidth))
for f in range(1, len(self.xlabels)):
#vertical
g.add(
Line(strokeColor=self.gridColor,
strokeWidth=self.strokeWidth,
x1=self.x + f * self.gridDivWidth,
y1=self.y,
x2=self.x + f * self.gridDivWidth,
y2=self.y + len(self.ylabels) * self.gridDivWidth))
# draw the 'dot'
g.add(
Circle(strokeColor=self.gridColor,
strokeWidth=self.strokeWidth,
fillColor=self.dotColor,
cx=self.x + (self.dotXPosition * self.gridDivWidth),
cy=self.y + (self.dotYPosition * self.gridDivWidth),
r=self.dotDiameter / 2.0))
#used for centering y-labels (below)
ascent = getFont(self.labelFontName).face.ascent
if ascent == 0:
ascent = 0.718 # default (from helvetica)
ascent = ascent * self.labelFontSize # normalize
#do y-labels
if self.ylabels != None:
for f in range(len(self.ylabels) - 1, -1, -1):
if self.ylabels[f] != None:
g.add(
String(strokeColor=self.gridColor,
text=self.ylabels[f],
fontName=self.labelFontName,
fontSize=self.labelFontSize,
fillColor=_PCMYK_black,
x=self.x - self.labelOffset,
y=self.y + (f * self.gridDivWidth +
(self.gridDivWidth - ascent) / 2.0),
textAnchor='end'))
#do x-labels
if self.xlabels != None:
for f in range(0, len(self.xlabels)):
if self.xlabels[f] != None:
l = Label()
l.x = self.x + (f * self.gridDivWidth
) + (self.gridDivWidth + ascent) / 2.0
l.y = self.y + (len(self.ylabels) *
self.gridDivWidth) + self.labelOffset
l.angle = 90
l.textAnchor = 'start'
l.fontName = self.labelFontName
l.fontSize = self.labelFontSize
l.fillColor = _PCMYK_black
l.setText(self.xlabels[f])
l.boxAnchor = 'sw'
l.draw()
g.add(l)
return g
def half_year(title,city, year, startmon):
'''startmon is the 1-indexed month to start the page on'''
reqd, mons = get_months(year, startmon)
LEFTMARGIN = 5
DAYCOLWIDTH = 50
CELLWIDTH = 80
CELLHEIGHT = 19
TOPROWHEIGHT = 18
WIDTH = LEFTMARGIN + DAYCOLWIDTH + CELLWIDTH*6
HEIGHT = reqd * CELLHEIGHT + TOPROWHEIGHT
d = shapes.Drawing(WIDTH, HEIGHT)
lab = Label()
lab.setOrigin(LEFTMARGIN,HEIGHT)
lab.boxAnchor = 'nw'
lab.setText(title)
lab.fontName = 'Times-Bold'
d.add(lab)
# Month headings
for i in range(6):
x = LEFTMARGIN + i*CELLWIDTH + DAYCOLWIDTH + CELLWIDTH/2
month_name = calendar.month_abbr[i + startmon]
d.add(shapes.String(x, HEIGHT-14, month_name,
fontSize=14, fontName='Times-Bold', textAnchor='middle'))
# Day row headings
for i in range(reqd):
y = HEIGHT - i*CELLHEIGHT - TOPROWHEIGHT
weekday_name = calendar.day_abbr[i%7]
d.add(shapes.String(LEFTMARGIN + 10, y-14, weekday_name,
fontSize=14))
# Draw the day cells, for each month
for j in range(6):
x = LEFTMARGIN + j*CELLWIDTH + DAYCOLWIDTH
# for each day
for i in range(reqd):
if i >= len(mons[j]) or not mons[j][i]:
continue
y = HEIGHT - i*CELLHEIGHT - TOPROWHEIGHT
# cells for each day, light grey background if weekend
weekend = i%7 > 4
lightgrey = colors.HexColor(0xD0B090)
color = weekend and lightgrey or colors.white
# Now we have (x, y, color) for (year, month=j+startmon, day=mons[j][i])
# Get the ephemerides for the date
date = datetime.datetime(year, j+startmon, mons[j][i])
(sunrise, sunset, moon_phase, moon_fm) = ephem3.ephem_one_day(city, date)
# Insert the date cell at x, y
d.add(shapes.Rect(x, y, CELLWIDTH, -CELLHEIGHT, fillColor=color))
d.add(shapes.String(x+1, y-10, str(mons[j][i]), fontSize=10))
green = colors.HexColor(0x207020)
# Insert the moon phase
if moon_fm:
d.add(shapes.String(x+15, y-10, moon_fm, fontSize=8, fillColor=green))
# for each day
# for each month
return d
def draw_hex(self):
print 'Reporting Hex'
story = []
for p in self.world.packets:
pl,t = p.build_ps()
XSTART = 0
XDSTART = 210
y = 0.0
XMUL= 100.0
YMUL = 10.0
larg = 16
YDUMP = PAGE_HEIGHT*0.80/YMUL - 10
YDUMP = 0
canvas = shapes.Drawing(500, 100)
# canvas.add(shapes.Rect(0,0, 500, PAGE_HEIGHT, fillColor=colors.yellow))
backcolor=colgen(0.6, 0.8, 1.0)
forecolor=colgen(0.2, 0.5, 0.8)
def hexstr(x):
s = []
for c in x:
s.append("%02x" % ord(c))
return " ".join(s)
my_y = 0
shift = 0
last_x = 0
while t:
bkcol = backcolor.next()
proto,fields = t.pop()
l = Label()
l.setText(proto.name)
l.boxAnchor = 'w'
l.boxStrokeColor = colors.gray
bc = colors.Color(bkcol[0], bkcol[1], bkcol[2] )
l.boxFillColor = bc
l.setOrigin(XSTART, (YDUMP-y)*YMUL)
canvas.add(l)
my_y = y
for fname, fval, fdump in fields:
y += 1.5
col = forecolor.next()
l = Label()
l.boxAnchor = 'w'
l.setText(fname.name)
l.setOrigin(XSTART + (0.1 * XMUL), (YDUMP-y)*YMUL)
canvas.add(l)
if fval is not None:
if len(fval) > 24:
fval = fval[:21]+"..."
else:
fval=""
l = Label()
l.setText(fval)
xlabel, ylabel = XSTART+(1.5*XMUL), (YDUMP-y)*YMUL
l.setOrigin(xlabel, ylabel)
l.boxStrokeWidth = 2
l.boxAnchor = 'e'
canvas.add(l)
first = True
while fdump:
dmp, fdump = fdump[:larg-shift],fdump[larg-shift:]
l = Label()
l.boxAnchor = 'w'
l.fontName = 'Courier'
l.boxFillColor = colors.Color(bkcol[0], bkcol[1], bkcol[2])
l.boxStrokeColor = colors.Color(col[0], col[1], col[2])
l.boxStrokeWidth = 2
xdump, ydump = XDSTART+ last_x * 0.06*XMUL, (YDUMP-my_y)*YMUL
l.setOrigin(xdump, ydump)
h = hexstr(dmp)
l.setText(h)
canvas.add(l)
if first:
link = shapes.Line(xdump, ydump, xlabel, ylabel, strokeColor=colors.Color(col[0], col[1], col[2]), strokeWidth=1)
canvas.add(link)
first = False
shift += len(dmp)
last_x += len(h) +1
if shift >= larg:
shift = 0
last_x = 0
my_y += 2
y += 2
scale = 0.7
canvas.shift(0, y * YMUL*scale)
canvas.height = min(y * YMUL *scale , PAGE_HEIGHT*0.80)
canvas.scale(scale, scale)
# para = Paragraph('<a name="hex%d"/>'%p.number + \
# '<a href="#summary%d">(%d) %s</a>' % (p.number, p.number, p.description), styles['Normal'])
# story.append([[para, Spacer(1,10), canvas]])
para = Paragraph('<a href="#summary%d">(%d) %s</a>' % (p.number, p.number, p.description), styles['Normal'])
story.append([[para, Spacer(1,10), canvas]])
t = Table(story)
t.setStyle(TableStyle([
('INNERGRID', (0,0), (-1,-1), 0.1, colors.black),
('BOX', (0,0), (-1,-1), 0.1, colors.black),
]))
return [t]
d.add(lab)
""")
from reportlab.graphics import shapes
from reportlab.graphics.charts.textlabels import Label
d = Drawing(200, 100)
# mark the origin of the label
d.add(Circle(100,90, 5, fillColor=colors.green))
lab = Label()
lab.setOrigin(100,90)
lab.boxAnchor = 'ne'
lab.angle = 45
lab.dx = 0
lab.dy = -20
lab.boxStrokeColor = colors.green
lab.setText('Some\nMulti-Line\nLabel')
d.add(lab)
draw(d, 'Label example')
disc("""
In the drawing above, the label is defined relative to the green blob.
The text box should have its north-east corner ten points down from
def draw(self):
g = Group()
#box
g.add(Rect(self.x,self.y,len(self.xlabels)*self.gridDivWidth,len(self.ylabels)*self.gridDivWidth,
strokeColor=self.gridColor,
strokeWidth=self.strokeWidth,
fillColor=None))
#internal gridding
for f in range (1,len(self.ylabels)):
#horizontal
g.add(Line(strokeColor=self.gridColor,
strokeWidth=self.strokeWidth,
x1 = self.x,
y1 = self.y+f*self.gridDivWidth,
x2 = self.x+len(self.xlabels)*self.gridDivWidth,
y2 = self.y+f*self.gridDivWidth))
for f in range (1,len(self.xlabels)):
#vertical
g.add(Line(strokeColor=self.gridColor,
strokeWidth=self.strokeWidth,
x1 = self.x+f*self.gridDivWidth,
y1 = self.y,
x2 = self.x+f*self.gridDivWidth,
y2 = self.y+len(self.ylabels)*self.gridDivWidth))
# draw the 'dot'
g.add(Circle(strokeColor=self.gridColor,
strokeWidth=self.strokeWidth,
fillColor=self.dotColor,
cx = self.x+(self.dotXPosition*self.gridDivWidth),
cy = self.y+(self.dotYPosition*self.gridDivWidth),
r = self.dotDiameter/2.0))
#used for centering y-labels (below)
ascent=getFont(self.labelFontName).face.ascent
if ascent==0:
ascent=0.718 # default (from helvetica)
ascent=ascent*self.labelFontSize # normalize
#do y-labels
if self.ylabels != None:
for f in range (len(self.ylabels)-1,-1,-1):
if self.ylabels[f]!= None:
g.add(String(strokeColor=self.gridColor,
text = self.ylabels[f],
fontName = self.labelFontName,
fontSize = self.labelFontSize,
fillColor=_PCMYK_black,
x = self.x-self.labelOffset,
y = self.y+(f*self.gridDivWidth+(self.gridDivWidth-ascent)/2.0),
textAnchor = 'end'))
#do x-labels
if self.xlabels != None:
for f in range (0,len(self.xlabels)):
if self.xlabels[f]!= None:
l=Label()
l.x=self.x+(f*self.gridDivWidth)+(self.gridDivWidth+ascent)/2.0
l.y=self.y+(len(self.ylabels)*self.gridDivWidth)+self.labelOffset
l.angle=90
l.textAnchor='start'
l.fontName = self.labelFontName
l.fontSize = self.labelFontSize
l.fillColor = _PCMYK_black
l.setText(self.xlabels[f])
l.boxAnchor = 'sw'
l.draw()
g.add(l)
return g
legend.fontName = 'Helvetica'
legend.fontSize = 8
legend.dxTextSpace = 5
legend.dy = 5
legend.dx = 5
legend.deltay = 5
legend.alignment = 'right'
drawing.add(lp)
drawing.add(legend)
if title != None:
label = Label()
label.x = w
label.y = h - 25
label.boxAnchor = 'se'
label.fontName = 'Helvetica'
label.fontSize = 10
label.setText(title)
drawing.add(label)
return drawing
def drawTable(self, data):
t = Table(data, None, None, None, 1, 1, 1)
extraStyle = []
for i in range(len(data[1:])):
if data[1:][i][0] == 'Free' or data[1:][i][0] == 'Used':
extraStyle.append(
('BACKGROUND', (0, i + 1), (-1, i + 1), colors.orange))
if data[1:][i][0] == 'SwapUsage' or data[1:][i][0] == 'LMK File':
extraStyle.append(
def addCompoundFeature(drawing, xmap, y, gene,
strokeColor=None, fillColor=colors.blue,
intronColor=colors.blue, intronWidth=0.5,
glyph=Block, height=12, utrHeight=6,
labeldy=10, fontSize=10, textAnchor='middle', boxAnchor='s'):
"""Adds a compund feature to the drawing.
A compound feature is typically several exons joined by zig-zag lines."""
rise = height + utrHeight
intronStarts = [None]
intronEnds = []
heights = []
for exon in gene:
x1,x2 = xmap(exon.start), xmap(exon.end)
kind = exon.kind.lower()
if kind in ['exon', 'utr']:
intronStarts.append(exon.end)
intronEnds.append(exon.start)
g = glyph()
g.x = x1
g.y = y+height/2
if exon.kind.lower()=='exon':
g.height = height
heights.append(height)
else:
g.height = utrHeight
heights.append(utrHeight)
g.length = x2-x1
g.fillColor = fillColor
if strokeColor:
g.strokeColor = strokeColor
else:
g.strokeColor = fillColor
g.fontSize = fontSize
drawing.add(g)
for i,(intronStart,intronEnd) in enumerate(zip(intronStarts[1:], intronEnds[1:])):
x1 = xmap(intronStart)
x2 = xmap(0.5*(intronStart+intronEnd))
x3 = xmap(intronEnd)
# if abs(x3-x1)<3: continue
# print intronStart,intronEnd,heights[i],heights[i+1]
y1 = y+heights[i]/2+height/2
y2 = y+rise
y3 = y+heights[i+1]/2+height/2
line1 = Line(x1,y1,x2,y2,strokeColor=intronColor,strokeWidth=intronWidth)
line2 = Line(x2,y2,x3,y3,strokeColor=intronColor,strokeWidth=intronWidth)
drawing.add(line1)
drawing.add(line2)
# Draw arrows
if xmap.flipped:
signum = -1
else:
signum = 1
if gene.strand=='+':
x1 = xmap(gene.end)
x2 = x1 + signum*15
x3 = x1 + signum*10
y1 = y + 0.5*height
y2 = y + 0.75*height
y3 = y + 0.25*height
line1 = Line(x1,y1,x2,y1,strokeColor=intronColor,strokeWidth=intronWidth)
line2 = Line(x2,y1,x3,y2,strokeColor=intronColor,strokeWidth=intronWidth)
line3 = Line(x2,y1,x3,y3,strokeColor=intronColor,strokeWidth=intronWidth)
drawing.add(line1)
drawing.add(line2)
drawing.add(line3)
else:
x1 = xmap(gene.start)
x2 = x1 - signum*15
x3 = x1 - signum*10
y1 = y + 0.5*height
y2 = y + 0.75*height
y3 = y + 0.25*height
line1 = Line(x1,y1,x2,y1,strokeColor=intronColor,strokeWidth=intronWidth)
line2 = Line(x2,y1,x3,y2,strokeColor=intronColor,strokeWidth=intronWidth)
line3 = Line(x2,y1,x3,y3,strokeColor=intronColor,strokeWidth=intronWidth)
drawing.add(line1)
drawing.add(line2)
drawing.add(line3)
# if gene has attribute name...
label = Label()
label.setText(gene.name)
pos = 0.5*(gene.start+gene.end)
x = xmap(pos)
label.setOrigin(x,y)
label.dy = labeldy
label.textAnchor = textAnchor
label.boxAnchor = boxAnchor
drawing.add(label)
