class OWDisplayMotifs(OWWidget):
settingsList = []
def __init__(self, parent=None, signalManager=None):
OWWidget.__init__(self, parent, signalManager, "&Display Motifs", 0)
# set default settings
self.colorBy = None
self.pvalThresholdIndex = None
self.pvalThreshold = None
#load settings
self.loadSettings()
# GUI
self.graph = OWGraph(self.mainArea)
self.graph.setYRlabels(None)
self.graph.enableGridXB(0)
self.graph.enableGridYL(1)
self.graph.setAxisMaxMinor(QwtPlot.xBottom, 10)
self.graph.setAxisMaxMajor(QwtPlot.xBottom, 10)
self.graph.setAxisAutoScale(QwtPlot.xBottom)
self.graph.setAxisScale(QwtPlot.xBottom, -1020, 0, 0)
self.mainArea.layout().addWidget(self.graph)
# inputs
# data and graph temp variables
self.inputs = [("Examples", ExampleTable, self.cdata, Default),
("Genes", list, self.newGeneList, Default),
("Motifs", list, self.newMotifList, Default)]
self.data = None
self.motifLines = []
self.visibleValues = []
self.valueToCurve = {}
self.allGenes = [] ## genes displayed always in same order
self.geneList = [] ## selected genes
self.motifList = [] ## selected motifs
self.valuesPresentInData = []
self.clusterPostProbThreshold = 0
# GUI
self.selValues = OWGUI.widgetBox(self.controlArea, "Values")
self.selcolorBy = OWGUI.widgetBox(self.controlArea, "Color By")
self.colorByCombo = OWGUI.comboBox(self.selcolorBy,
self,
"colorBy",
items=[],
callback=self.colorByChanged)
self.pvalThresholdCombo = OWGUI.comboBox(
self.selValues,
self,
"pvalThresholdIndex",
items=[],
callback=self.pvalThresholdChanged)
self.valuesQLB = QListWidget(self.selValues)
self.valuesQLB.setSelectionMode(QListWidget.MultiSelection)
self.connect(self.valuesQLB, SIGNAL("itemSelectionChanged()"),
self.valuesSelectionChange)
self.selValues.layout().addWidget(self.valuesQLB)
self.unselectAllQLB = OWGUI.button(self.selValues,
self,
"Unselect all",
callback=self.unselAll)
def unselAll(self):
self.valuesQLB.clearSelection()
def pvalThresholdChanged(self):
print self.pvalThresholdIndex
if self.pvalThresholdIndex:
self.pvalThreshold = float(
self.pvalThresholdCombo.text(self.pvalThresholdIndex))
else:
self.pvalThreshold = None
self.calcMotifsGraph()
self.updateMotifsGraph()
def valuesSelectionChange(self):
visibleOutcomes = []
for i in range(self.valuesQLB.count()):
item = self.valuesQLB.item(i)
if item.isSelected():
visibleOutcomes.append(str(item.text()))
self.visibleValues = visibleOutcomes
self.updateMotifsGraph()
def updateSelectionChange(self):
## make new colors only for those colorBy values present in data
colors = ColorPaletteHSV(len(self.valuesPresentInData))
for (i, v) in enumerate(self.valuesPresentInData):
curve = self.valueToCurve[v]
curve.color = colors[i]
self.setValuesNames(self.valuesPresentInData)
for i in range(self.valuesQLB.count()):
item = self.valuesQLB.item(i)
item.setSelected(str(item.text()) in self.visibleValues)
# else:
# self.valuesQLB.setSelected(i, 0)
def colorByChanged(self):
# self.graph.removeCurves()
self.graph.removeDrawingCurves()
self.valueToCurve = {}
if self.colorBy == None:
self.setValuesNames(None)
return
if self.potentialColorVariables:
var = self.potentialColorVariables[self.colorBy]
values = sorted(var.values)
# values.sort()
## generate colors for each colorby value (each color on its own curve)
colors = ColorPaletteHSV(len(values))
for (i, v) in enumerate(values):
## create curve in graph
curve = subBarQwtPlotCurve()
curve.color = colors[i]
curve.attach(self.graph)
# ckey = self.graph.insertCurve(curve)
curve.setStyle(QwtPlotCurve.UserCurve)
self.valueToCurve[v] = curve
self.setValuesNames(values)
self.calcMotifsGraph()
def setValuesNames(self, values):
self.valuesQLB.clear()
if values == None:
return
for v in values:
self.valuesQLB.addItem(
QListWidgetItem(QIcon(ColorPixmap(self.valueToCurve[v].color)),
v))
self.valuesQLB.item(self.valuesQLB.count() - 1).setSelected(True)
## signal processing
def newGeneList(self, list):
self.geneList = []
if list is not None:
self.geneList = list
self.calcMotifsGraph()
self.updateMotifsGraph()
def newMotifList(self, list):
self.motifList = []
if list is not None:
self.motifList = list
self.calcMotifsGraph()
self.updateMotifsGraph()
def cdata(self, data):
self.data = data
self.motifLines = []
self.colorByCombo.clear()
if self.data == None:
self.colorBy = None
self.potentialColorVariables = []
self.colorByChanged()
self.graph.setYLlabels(None)
else:
self.potentialColorVariables = [v for v in self.data.domain.variables + self.data.domain.getmetas().values() \
if v.varType == orange.VarTypes.Discrete]
for var in self.potentialColorVariables:
self.colorByCombo.addItem(str(var.name))
## break motif info according to gene (sequenceID)
self.motifLines = defaultdict(list)
for e in self.data:
geneID = str(e['sequenceID'])
self.motifLines[geneID].append(e)
self.allGenes = sorted(self.motifLines.keys())
if self.potentialColorVariables:
self.colorBy = min(
len(self.potentialColorVariables) - 1, self.colorBy or 0)
else:
self.colorBy = None
self.colorByChanged()
if len(self.potentialColorVariables) > 0:
self.colorByCombo.setCurrentIndex(0)
## update graph
def calcMotifsGraph(self):
graphData = {}
for (colorKey, curve) in self.valueToCurve.iteritems():
graphData[colorKey] = [[], []]
lineCn = 0
yVals = []
self.colorByValuesPresentInData = []
self.valuesPresentInData = []
for lineKey in self.geneList:
## if (self.geneList <> None) and (self.geneList <> []) and (lineKey not in self.geneList): continue
yVals.append(lineKey)
for e in self.motifLines[lineKey]:
motifName = str(e['motifName']) #.value
if self.motifList is not None and self.motifList != [] and motifName not in self.motifList:
continue
motifDistToEnd = -int(e['distToEnd']) #.value)
postProb = int(round(float(e['pvalue']) * 100))
dir = str(e['direction'])
if 1 or (
postProb >= self.clusterPostProbThreshold
): ## and (chiSquare >= self.motifChiSquareThreshold):
colorAttr = self.potentialColorVariables[self.colorBy]
colorKey = str(e[colorAttr])
if colorKey not in self.valuesPresentInData:
self.valuesPresentInData.append(colorKey)
# print motifNumber, colorKey
# set the point x values
graphData[colorKey][0].append(motifDistToEnd)
graphData[colorKey][0].append(motifDistToEnd + 5.0)
# set the point y values
if dir == "1":
graphData[colorKey][1].append(lineCn + 0.0)
graphData[colorKey][1].append(lineCn + 0.30)
elif dir == "-1":
graphData[colorKey][1].append(lineCn - 0.30)
graphData[colorKey][1].append(lineCn + 0.0)
else:
graphData[colorKey][1].append(lineCn - 0.30)
graphData[colorKey][1].append(lineCn + 0.30)
lineCn += 1
vals = reduce(list.__add__, [val[0] for val in graphData.itervalues()],
[])
minX = min(vals or [0]) - 5.0
maxX = max(vals or [0]) + 5.0
self.graph.setYLlabels(yVals)
self.graph.setAxisScale(QwtPlot.yLeft, -0.5, len(yVals) - 0.5, 1)
self.graph.setAxisScale(QwtPlot.xBottom, minX, maxX)
for (colorKey, curve) in self.valueToCurve.iteritems():
curve.setData(graphData[colorKey][0], graphData[colorKey][1])
curve.setVisible(colorKey in self.visibleValues)
self.graph.replot()
self.valuesPresentInData.sort()
self.visibleValues = [v for v in self.valuesPresentInData]
self.updateSelectionChange()
def updateMotifsGraph(self):
for (colorKey, curve) in self.valueToCurve.items():
curve.setVisible(colorKey in self.visibleValues)
self.graph.replot()
class OWDisplayMotifs(OWWidget):
settingsList = []
def __init__(self,parent=None, signalManager = None):
OWWidget.__init__(self, parent, signalManager, "&Display Motifs", 0)
# set default settings
self.colorBy = None
self.pvalThresholdIndex = None
self.pvalThreshold = None
#load settings
self.loadSettings()
# GUI
self.graph = OWGraph(self.mainArea)
self.graph.setYRlabels(None)
self.graph.enableGridXB(0)
self.graph.enableGridYL(1)
self.graph.setAxisMaxMinor(QwtPlot.xBottom, 10)
self.graph.setAxisMaxMajor(QwtPlot.xBottom, 10)
self.graph.setAxisAutoScale(QwtPlot.xBottom)
self.graph.setAxisScale(QwtPlot.xBottom, -1020, 0, 0)
self.mainArea.layout().addWidget(self.graph)
# inputs
# data and graph temp variables
self.inputs = [("Examples", ExampleTable, self.cdata, Default), ("Genes", list, self.newGeneList, Default), ("Motifs", list, self.newMotifList, Default)]
self.data = None
self.motifLines = []
self.visibleValues = []
self.valueToCurve = {}
self.allGenes = [] ## genes displayed always in same order
self.geneList = [] ## selected genes
self.motifList = [] ## selected motifs
self.valuesPresentInData = []
self.clusterPostProbThreshold = 0
# GUI
self.selValues = OWGUI.widgetBox(self.controlArea, "Values")
self.selcolorBy = OWGUI.widgetBox(self.controlArea, "Color By")
self.colorByCombo = OWGUI.comboBox(self.selcolorBy, self, "colorBy",
items=[],
callback=self.colorByChanged)
self.pvalThresholdCombo = OWGUI.comboBox(self.selValues, self, "pvalThresholdIndex",
items=[],
callback=self.pvalThresholdChanged)
self.valuesQLB = QListWidget(self.selValues)
self.valuesQLB.setSelectionMode(QListWidget.MultiSelection)
self.connect(self.valuesQLB, SIGNAL("itemSelectionChanged()"), self.valuesSelectionChange)
self.selValues.layout().addWidget(self.valuesQLB)
self.unselectAllQLB = OWGUI.button(self.selValues, self, "Unselect all",
callback = self.unselAll)
def unselAll(self):
self.valuesQLB.clearSelection()
def pvalThresholdChanged(self):
print self.pvalThresholdIndex
if self.pvalThresholdIndex:
self.pvalThreshold = float(self.pvalThresholdCombo.text(self.pvalThresholdIndex))
else:
self.pvalThreshold = None
self.calcMotifsGraph()
self.updateMotifsGraph()
def valuesSelectionChange(self):
visibleOutcomes = []
for i in range(self.valuesQLB.count()):
item = self.valuesQLB.item(i)
if item.isSelected():
visibleOutcomes.append(str(item.text()))
self.visibleValues = visibleOutcomes
self.updateMotifsGraph()
def updateSelectionChange(self):
## make new colors only for those colorBy values present in data
colors = ColorPaletteHSV(len(self.valuesPresentInData))
for (i, v) in enumerate(self.valuesPresentInData):
curve = self.valueToCurve[v]
curve.color = colors[i]
self.setValuesNames(self.valuesPresentInData)
for i in range(self.valuesQLB.count()):
item = self.valuesQLB.item(i)
item.setSelected(str(item.text()) in self.visibleValues)
# else:
# self.valuesQLB.setSelected(i, 0)
def colorByChanged(self):
# self.graph.removeCurves()
self.graph.removeDrawingCurves()
self.valueToCurve = {}
if self.colorBy == None:
self.setValuesNames(None)
return
if self.potentialColorVariables:
var = self.potentialColorVariables[self.colorBy]
values = sorted(var.values)
# values.sort()
## generate colors for each colorby value (each color on its own curve)
colors = ColorPaletteHSV(len(values))
for (i, v) in enumerate(values):
## create curve in graph
curve = subBarQwtPlotCurve()
curve.color = colors[i]
curve.attach(self.graph)
# ckey = self.graph.insertCurve(curve)
curve.setStyle(QwtPlotCurve.UserCurve)
self.valueToCurve[v] = curve
self.setValuesNames(values)
self.calcMotifsGraph()
def setValuesNames(self, values):
self.valuesQLB.clear()
if values == None:
return
for v in values:
self.valuesQLB.addItem(QListWidgetItem(QIcon(ColorPixmap(self.valueToCurve[v].color)), v))
self.valuesQLB.item(self.valuesQLB.count() - 1).setSelected(True)
## signal processing
def newGeneList(self, list):
self.geneList = []
if list is not None:
self.geneList = list
self.calcMotifsGraph()
self.updateMotifsGraph()
def newMotifList(self, list):
self.motifList = []
if list is not None:
self.motifList = list
self.calcMotifsGraph()
self.updateMotifsGraph()
def cdata(self, data):
self.data = data
self.motifLines = []
self.colorByCombo.clear()
if self.data == None:
self.colorBy = None
self.potentialColorVariables = []
self.colorByChanged()
self.graph.setYLlabels(None)
else:
self.potentialColorVariables = [v for v in self.data.domain.variables + self.data.domain.getmetas().values() \
if v.varType == orange.VarTypes.Discrete]
for var in self.potentialColorVariables:
self.colorByCombo.addItem(str(var.name))
## break motif info according to gene (sequenceID)
self.motifLines = defaultdict(list)
for e in self.data:
geneID = str(e['sequenceID'])
self.motifLines[geneID].append(e)
self.allGenes = sorted(self.motifLines.keys())
if self.potentialColorVariables:
self.colorBy = min(len(self.potentialColorVariables) - 1, self.colorBy or 0)
else:
self.colorBy = None
self.colorByChanged()
if len(self.potentialColorVariables) > 0:
self.colorByCombo.setCurrentIndex(0)
## update graph
def calcMotifsGraph(self):
graphData = {}
for (colorKey, curve) in self.valueToCurve.iteritems():
graphData[colorKey] = [[], []]
lineCn = 0
yVals = []
self.colorByValuesPresentInData = []
self.valuesPresentInData = []
for lineKey in self.geneList:
## if (self.geneList <> None) and (self.geneList <> []) and (lineKey not in self.geneList): continue
yVals.append( lineKey)
for e in self.motifLines[lineKey]:
motifName = str(e['motifName'])#.value
if self.motifList is not None and self.motifList != [] and motifName not in self.motifList:
continue
motifDistToEnd = -int(e['distToEnd']) #.value)
postProb = int(round(float(e['pvalue']) * 100))
dir = str(e['direction'])
if 1 or (postProb >= self.clusterPostProbThreshold): ## and (chiSquare >= self.motifChiSquareThreshold):
colorAttr = self.potentialColorVariables[self.colorBy]
colorKey = str(e[colorAttr])
if colorKey not in self.valuesPresentInData:
self.valuesPresentInData.append(colorKey)
# print motifNumber, colorKey
# set the point x values
graphData[colorKey][0].append(motifDistToEnd)
graphData[colorKey][0].append(motifDistToEnd + 5.0)
# set the point y values
if dir == "1":
graphData[colorKey][1].append(lineCn + 0.0)
graphData[colorKey][1].append(lineCn + 0.30)
elif dir == "-1":
graphData[colorKey][1].append(lineCn - 0.30)
graphData[colorKey][1].append(lineCn + 0.0)
else:
graphData[colorKey][1].append(lineCn - 0.30)
graphData[colorKey][1].append(lineCn + 0.30)
lineCn += 1
vals = reduce(list.__add__, [val[0] for val in graphData.itervalues()], [])
minX = min(vals or [0]) - 5.0
maxX = max(vals or [0]) + 5.0
self.graph.setYLlabels(yVals)
self.graph.setAxisScale(QwtPlot.yLeft, -0.5, len(yVals) - 0.5, 1)
self.graph.setAxisScale(QwtPlot.xBottom, minX, maxX)
for (colorKey, curve) in self.valueToCurve.iteritems():
curve.setData(graphData[colorKey][0], graphData[colorKey][1])
curve.setVisible(colorKey in self.visibleValues)
self.graph.replot()
self.valuesPresentInData.sort()
self.visibleValues = [v for v in self.valuesPresentInData]
self.updateSelectionChange()
def updateMotifsGraph(self):
for (colorKey, curve) in self.valueToCurve.items():
curve.setVisible(colorKey in self.visibleValues)
self.graph.replot()
