class Chart(JPanel):
def _createEmptyChart(self, dataset=None):
if self.isTemporal:
hText = "Hs"
fText = "Fgt"
else:
hText = "He"
fText = "Fst"
chart = ChartFactory.createXYLineChart(
self.title, # chart title
hText, # x axis label
fText, # y axis label
dataset, # data
PlotOrientation.VERTICAL,
True, # include legend
True, # tooltips
False # urls
)
chart.setBackgroundPaint(Color.white)
# get a reference to the plot for further customisation...
# change the auto tick unit selection to integer units only...
#rangeAxis = plot.getRangeAxis()
#rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits())
self.confArea = None
return chart
def setSelLoci(self, pv, allLoci, selLoci):
self.pv = pv
self.allLoci = allLoci
self.selLoci = selLoci
self.drawLabels()
def drawLabels(self):
if not hasattr(self, 'pv'): return
plot = self.chart.getPlot()
plot.clearAnnotations()
red = 0
for i in range(len(self.valMarkers)):
if not self.valMarkers[i]:
red += 1
continue
if self.allLoci[i] in self.selLoci:
if not self.labelSelected: continue
else:
if not self.labelNeutral: continue
x = self.pv[i - red][0]
y = self.pv[i - red][1]
locus = self.allLoci[i]
note = XYTextAnnotation(locus, x + 0.002, y + 0.002)
note.setTextAnchor(TextAnchor.BOTTOM_LEFT)
plot.addAnnotation(note)
def setMarkers(self, markers):
self.markers = XYSeries("Markers")
self.maxX = 0.0
self.maxY = 0.0
self.minY = -0.05
self.out = []
self.valMarkers = markers
for marker in markers:
if not marker:
continue
if marker[0] < 2 and marker[0] > self.maxX:
self.maxX = marker[0]
if marker[1] < 2 and marker[1] > self.maxY:
self.maxY = marker[1]
if marker[1] > -2 and marker[1] < self.minY:
self.minY = marker[1]
#self.markers.add(marker[0], max([0.0, marker[1]]))
self.markers.add(marker[0], marker[1])
self.maxX = max([0.501, self.maxX + 0.001])
self.maxX = min([1, self.maxX])
self.maxY += 0.05
self.minY -= 0.05
def setTop(self, markers):
#setBottom has to be done before, as setMarkers
self.top = YIntervalSeries("Candidate neutral")
self.limit = YIntervalSeries("Candidate positive selection")
if len(markers) > 1:
#if self.maxY > markers[0][1]:
# self.limit.add(0.0, markers[0][1], markers[0][0], markers[0][1])
#else: #It does not really matter
# self.limit.add(0.0, -1, 1.1, 1.1)
self.limit.add(0.0, markers[0][1], markers[0][1], 1.1)
for i in range(len(markers)):
self.top.add(markers[i][0], self.bottomList[i][1],
self.bottomList[i][1], markers[i][1])
if self.maxY > markers[i][1]:
self.limit.add(markers[i][0], markers[i][1], markers[i][1],
1.1)
else: #It does not really matter
self.limit.add(markers[i][0], markers[i][1], markers[i][1],
1.1)
#if markers[i][0] > self.maxX: break
#We do this at the end to fill the whole graphic
def setBottom(self, markers):
#print markers
self.bottomList = map(lambda (x, y): (x, y),
markers) #legacy, can remove...
self.bottom = YIntervalSeries("Candidate balancing selection")
if len(markers) > 0:
self.bottom.add(0.0, -1.0, -1.0, self.bottomList[0][1])
for marker in self.bottomList:
self.bottom.add(marker[0], -1.0, -1.0, marker[1])
#if marker[0] > self.maxX: break
#We do this at the end to fill the whole graphic
def updateChartDataset(self, drawLabels=True):
dataset = XYSeriesCollection()
#self._calculateConfArea()
#dataset.addSeries(self.confArea)
dataset.addSeries(self.markers)
plot = self.chart.getPlot()
rangeAxis = plot.getRangeAxis()
domainAxis = plot.getDomainAxis()
rangeAxis.setRange(self.minY, self.maxY) #change
domainAxis.setRange(self.minX, self.maxX)
#plot.setBackgroundPaint(Color.lightGray);
#plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
#plot.setDomainGridlinePaint(Color.white);
#plot.setRangeGridlinePaint(Color.white);
markerRenderer = XYLineAndShapeRenderer(False, True)
#print self.markerColor
markerRenderer.setSeriesPaint(0, self.markerColor)
markerRenderer.setSeriesShape(0, Ellipse2D.Double(-3, -3, 6, 6))
#markerRenderer.setToolTipGenerator(FDistToolTipGenerator(self.pointNames))
plot.setRenderer(0, markerRenderer)
plot.setDataset(0, dataset)
dataset = XYSeriesCollection()
if self.drawCI:
dataset = YIntervalSeriesCollection()
CIRenderer = DeviationRenderer(True, False)
# CIRenderer.setOutline(True)
# CIRenderer.setRoundXCoordinates(True)
dataset.addSeries(self.bottom)
dataset.addSeries(self.top)
dataset.addSeries(self.limit)
CIRenderer.setSeriesFillPaint(0, self.balColor)
CIRenderer.setSeriesFillPaint(1, self.neuColor)
CIRenderer.setSeriesFillPaint(2, self.posColor)
CIRenderer.setSeriesPaint(0, self.balColor)
CIRenderer.setSeriesPaint(1, self.neuColor)
CIRenderer.setSeriesPaint(2, self.posColor)
plot.setDataset(1, dataset)
plot.setRenderer(1, CIRenderer)
plot.setDataset(1, dataset)
if drawLabels:
self.drawLabels()
def resetData(self, justAnnots=False):
if not justAnnots:
self.markers = XYSeries("Markers")
self.drawCI = False
self.chart.getPlot().clearAnnotations()
if hasattr(self, 'pv'):
del (self.pv)
self.updateChartDataset()
def save(self, parent, format):
chooser = JFileChooser()
# filter = FileNameExtensionFilter(
# format + " files",
# array([format, format.lower()], String))
# chooser.setFileFilter(filter);
returnVal = chooser.showSaveDialog(parent)
if returnVal == JFileChooser.APPROVE_OPTION:
fileName = chooser.getSelectedFile().getPath()
if not fileName.upper().endswith('.' + format):
fileName += '.' + format.lower()
file = File(fileName)
else:
return
if format == 'PNG':
ChartUtils.saveChartAsPNG(file, self.chart, self.exportX,
self.exportY)
elif format == 'SVG':
domImpl = GenericDOMImplementation.getDOMImplementation()
doc = domImpl.createDocument(None, "svg", None)
svgGen = SVGGraphics2D(doc)
svgGen.getGeneratorContext().setPrecision(6)
self.chart.draw(
svgGen, Rectangle2D.Double(0, 0, self.exportX, self.exportY),
None)
out = OutputStreamWriter(FileOutputStream(file), "UTF-8")
svgGen.stream(out, True) #True is for useCSS
out.close()
elif format == 'PDF':
mapper = DefaultFontMapper()
pageSize = Rectangle(self.exportX, self.exportY)
doc = TextDocument(pageSize, 50, 50, 50, 50)
out = BufferedOutputStream(FileOutputStream(file))
writer = PdfWriter.getInstance(doc, out)
doc.open()
cb = writer.getDirectContent()
tp = cb.createTemplate(self.exportX, self.exportY)
g2 = tp.createGraphics(self.exportX, self.exportY, mapper)
r2D = Rectangle2D.Double(0, 0, self.exportX, self.exportY)
self.chart.draw(g2, r2D)
g2.dispose()
cb.addTemplate(tp, 0, 0)
doc.close()
#out.close()
def __init__(self, width, height, isTemporal=False):
JPanel()
self.isTemporal = isTemporal
self.minY = 0.0 # -0.05
self.minX = 0.0 # -0.02
self.maxX = 0.5 # 0.52
self.maxY = 1.0
self.drawCI = False
if isTemporal:
self.title = "Fgt/Hs"
else:
self.title = "Fst/He"
self.labelSelected = True
self.labelNeutral = False
self.posColor = Color.RED
self.neuColor = Color.LIGHT_GRAY
self.balColor = Color.YELLOW
self.markerColor = Color.BLUE
self.exportX = width
self.exportY = height
self.chart = self._createEmptyChart()
self.chart.setAntiAlias(True)
self.resetData()
self.cp = ChartPanel(self.chart)
self.cp.setDisplayToolTips(True)
self.cp.setPreferredSize(Dimension(width, height))
self.add(self.cp)
class Chart(JPanel):
def _createEmptyChart(self, dataset = None):
chart = ChartFactory.createXYLineChart(
self.title, # chart title
"He", # x axis label
"Fst", # y axis label
dataset, # data
PlotOrientation.VERTICAL,
True, # include legend
True, # tooltips
False # urls
)
chart.setBackgroundPaint(Color.white)
# get a reference to the plot for further customisation...
# change the auto tick unit selection to integer units only...
#rangeAxis = plot.getRangeAxis()
#rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits())
self.confArea = None
return chart
def setSelLoci(self, pv, allLoci, selLoci):
self.pv = pv
self.allLoci = allLoci
self.selLoci = selLoci
self.drawLabels()
def drawLabels(self):
if not hasattr(self, 'pv'): return
plot = self.chart.getPlot()
plot.clearAnnotations()
red = 0
for i in range(len(self.valMarkers)):
if not self.valMarkers[i]:
red += 1
continue
if self.allLoci[i] in self.selLoci:
if not self.labelSelected: continue
else:
if not self.labelNeutral: continue
x = self.pv[i-red][0]
y = self.pv[i-red][1]
locus = self.allLoci[i]
note = XYTextAnnotation(locus, x + 0.002, y + 0.002)
note.setTextAnchor(TextAnchor.BOTTOM_LEFT)
plot.addAnnotation(note)
def setMarkers(self, markers):
self.markers = XYSeries("Markers")
self.maxX = 0.0
self.maxY = 0.0
self.minY = -0.05
self.out = []
self.valMarkers = markers
for marker in markers:
if not marker:
continue
if marker[0]<2 and marker[0] > self.maxX:
self.maxX = marker[0]
if marker[1]<2 and marker[1] > self.maxY:
self.maxY = marker[1]
if marker[1]>-2 and marker[1] < self.minY:
self.minY = marker[1]
#self.markers.add(marker[0], max([0.0, marker[1]]))
self.markers.add(marker[0], marker[1])
self.maxX += 0.1
self.maxX = min([1, self.maxX])
self.maxY += 0.05
self.minY -= 0.05
def setTop(self, markers):
#setBottom has to be done before, as setMarkers
self.top = YIntervalSeries("Candidate neutral")
self.limit = YIntervalSeries("Candidate positive selection")
if len(markers) > 1:
#if self.maxY > markers[0][1]:
# self.limit.add(0.0, markers[0][1], markers[0][0], markers[0][1])
#else: #It does not really matter
# self.limit.add(0.0, -1, 1.1, 1.1)
self.limit.add(0.0, markers[0][1], markers[0][1], 1.1)
for i in range(len(markers)):
self.top.add(markers[i][0], self.bottomList[i][1],self.bottomList[i][1],
markers[i][1] )
if self.maxY > markers[i][1]:
self.limit.add(markers[i][0], markers[i][1],markers[i][1],
1.1)
else: #It does not really matter
self.limit.add(markers[i][0], markers[i][1],markers[i][1], 1.1)
#if markers[i][0] > self.maxX: break
#We do this at the end to fill the whole graphic
def setBottom(self, markers):
#print markers
self.bottomList = map (
lambda (x,y): (x,y),
markers) #legacy, can remove...
self.bottom = YIntervalSeries("Candidate balancing selection")
if len(markers) > 0:
self.bottom.add(0.0, -1.0, -1.0, self.bottomList[0][1])
for marker in self.bottomList:
self.bottom.add(marker[0], -1.0, -1.0, marker[1])
#if marker[0] > self.maxX: break
#We do this at the end to fill the whole graphic
def updateChartDataset(self, drawLabels=True):
dataset = XYSeriesCollection()
#self._calculateConfArea()
#dataset.addSeries(self.confArea)
dataset.addSeries(self.markers)
plot = self.chart.getPlot()
rangeAxis = plot.getRangeAxis()
domainAxis = plot.getDomainAxis()
rangeAxis.setRange(self.minY, self.maxY) #change
domainAxis.setRange(0.0, self.maxX)
#plot.setBackgroundPaint(Color.lightGray);
#plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0));
#plot.setDomainGridlinePaint(Color.white);
#plot.setRangeGridlinePaint(Color.white);
markerRenderer = XYLineAndShapeRenderer(False, True)
#print self.markerColor
markerRenderer.setSeriesPaint(0, self.markerColor)
markerRenderer.setSeriesShape(0, Ellipse2D.Double(-3, -3, 6, 6))
#markerRenderer.setToolTipGenerator(FDistToolTipGenerator(self.pointNames))
plot.setRenderer(0, markerRenderer)
plot.setDataset(0, dataset)
dataset = XYSeriesCollection()
if self.drawCI:
dataset = YIntervalSeriesCollection()
CIRenderer = DeviationRenderer(True, False)
#CIRenderer.setOutline(True)
#CIRenderer.setRoundXCoordinates(True)
dataset.addSeries(self.bottom)
dataset.addSeries(self.top)
dataset.addSeries(self.limit)
CIRenderer.setSeriesFillPaint(0, self.balColor)
CIRenderer.setSeriesFillPaint(1, self.neuColor)
CIRenderer.setSeriesFillPaint(2, self.posColor)
CIRenderer.setSeriesPaint(0, self.balColor)
CIRenderer.setSeriesPaint(1, self.neuColor)
CIRenderer.setSeriesPaint(2, self.posColor)
plot.setDataset(1, dataset)
plot.setRenderer(1, CIRenderer)
plot.setDataset(1, dataset)
if drawLabels: self.drawLabels()
def resetData(self, justAnnots = False):
if not justAnnots:
self.markers = XYSeries("Markers")
self.drawCI = False
self.chart.getPlot().clearAnnotations()
if hasattr(self, 'pv'):
del(self.pv)
self.updateChartDataset()
def save(self, parent, format):
chooser = JFileChooser()
#filter = FileNameExtensionFilter(
# format + " files",
# array([format, format.lower()], String))
#chooser.setFileFilter(filter);
returnVal = chooser.showSaveDialog(parent)
if returnVal == JFileChooser.APPROVE_OPTION:
fileName = chooser.getSelectedFile().getPath()
if not fileName.upper().endswith('.' + format):
fileName += '.' + format.lower()
file = File(fileName)
else:
return
if format == 'PNG':
ChartUtilities.saveChartAsPNG(file, self.chart, self.exportX, self.exportY)
elif format == 'SVG':
domImpl = GenericDOMImplementation.getDOMImplementation()
doc = domImpl.createDocument(None, "svg", None)
svgGen = SVGGraphics2D(doc)
svgGen.getGeneratorContext().setPrecision(6)
self.chart.draw(svgGen,
Rectangle2D.Double(0, 0, self.exportX, self.exportY), None)
out = OutputStreamWriter(FileOutputStream(file), "UTF-8")
svgGen.stream(out, True) #True is for useCSS
out.close()
elif format == 'PDF':
mapper = DefaultFontMapper()
pageSize = Rectangle(self.exportX, self.exportY)
doc = TextDocument(pageSize, 50, 50, 50, 50)
out = BufferedOutputStream(FileOutputStream(file))
writer = PdfWriter.getInstance(doc, out)
doc.open()
cb = writer.getDirectContent()
tp = cb.createTemplate(self.exportX, self.exportY)
g2 = tp.createGraphics(self.exportX, self.exportY, mapper)
r2D = Rectangle2D.Double(0, 0, self.exportX, self.exportY)
self.chart.draw(g2, r2D)
g2.dispose()
cb.addTemplate(tp, 0, 0)
doc.close()
#out.close()
def __init__(self, width, height):
JPanel()
self.minY = -0.05
self.maxX = 1.0
self.maxY = 1.0
self.drawCI = False
self.title = "Fst/He"
self.labelSelected = True
self.labelNeutral = False
self.posColor = Color.RED
self.neuColor = Color.LIGHT_GRAY
self.balColor = Color.YELLOW
self.markerColor = Color.BLUE
self.exportX = width
self.exportY = height
self.chart = self._createEmptyChart()
self.chart.setAntiAlias(False)
self.resetData()
self.cp = ChartPanel(self.chart)
self.cp.setDisplayToolTips(True)
self.cp.setPreferredSize(Dimension(width, height))
self.add(self.cp)
