def __init__(self,
title1,
data1,
title2=None,
data2=None,
xLabel='Windows',
yLabel='RF Distance'):
Window.__init__(
self,
windowTitle='Robinson Foulds Distance From Species Tree',
legend=False)
if title2 == None:
self.plotter.stat_scatter(data1,
title1,
xLabel,
yLabel,
subplotPosition=111)
else:
self.plotter.stat_scatter(data1,
title1,
xLabel,
yLabel,
subplotPosition=211)
self.plotter.stat_scatter(data2,
title2,
xLabel,
yLabel,
subplotPosition=212)
self.show()
def __init__(self, title, windowsToTopologies, colors, heights):
Window.__init__(self, windowTitle='Windows to Top Topologies')
# plot
self.plotter.topologyScatter(title, windowsToTopologies, colors,
heights)
self.show()
def __init__(self, lWindows, sigArray):
Window.__init__(self, windowTitle='L Statistic Window')
self.plotter.sorted_scatter(lWindows, sigArray,
'Windows to Generalized D', 'Windows',
'Generalized D Values')
self.show()
def __init__(self, windowsToPGTST, title, xLabel='', yLabel=''):
Window.__init__(self,
windowTitle='P(gene tree | species tree)',
legend=False)
self.plotter.stat_scatter(windowsToPGTST, title, xLabel, yLabel)
self.show()
def __init__(self, seq1, seq2, confidenceThreshold, xLabel='', yLabel=''):
Window.__init__(self, windowTitle='Bootstrap Contraction Window')
self.plotter.doubleLineGraph(seq1,
seq2,
confidenceThreshold,
xLabel=xLabel,
yLabel=yLabel)
self.show()
def __init__(self, title, labels, sizes, donutColors):
Window.__init__(self,
windowTitle='Top Topology Frequency Donut',
x=600,
y=600)
# plot
self.plotter.topologyDonut(title, labels, sizes, donutColors)
self.show()
def __init__(self,
title,
data,
xLabel='Windows',
yLabel='% Informative Sites'):
Window.__init__(self,
windowTitle='Windows to Informative Sites',
legend=False)
self.plotter.stat_scatter(data, title, xLabel=xLabel, yLabel=yLabel)
self.show()
def __init__(self, title1, data1, xLabel1='', yLabel1='', groupLabels1=()):
Window.__init__(self, windowTitle='Percent Sites Matching')
self.plotter.barPlot(title1,
data1,
xLabel=xLabel1,
yLabel=yLabel1,
groupLabels=groupLabels1,
subplotPosition=111)
self.show()
def __init__(self, title, data, xLabel1='', yLabel1='', groupLabels1=()):
Window.__init__(self,
windowTitle='Robinson Foulds Distance From MS Truth')
self.plotter.nlineGraph(data,
title,
xLabel="Site Indices",
yLabel=yLabel1,
subplotPosition=111,
groupLabels1=groupLabels1)
self.show()
def __init__(self,
dWindows,
title='Windows to D Statistic',
xLabel='Window Indices',
yLabel='D Statistic values'):
Window.__init__(self, windowTitle='D Statistic Window')
self.plotter.stat_scatter(dWindows,
title,
xLabel=xLabel,
yLabel=yLabel)
self.show()
def __init__(self, title, sitesToInformative):
Window.__init__(self,
windowTitle='Informative Sites Heatmap',
legend=False)
self.connect(self.plotter, QtCore.SIGNAL('HEATMAP_COMPLETE'),
self.show)
self.plotter.plot = 'heatmap'
self.plotter.title = title
self.plotter.sitesToInformative = sitesToInformative
self.plotter.start()
def __init__(self,
title,
colorScheme,
topologies_to_counts,
rooted=False,
outGroup=False):
Window.__init__(self, windowTitle='All Trees Window', legend=False)
self.plotter.topologyColorizer(title,
colorScheme,
topologies_to_counts,
rooted=rooted,
outgroup=outGroup)
self.show()
def __init__(self, alignment, windowsToTopTopologies, topologiesToColors, windowSize, windowOffset, sitesToInformative):
Window.__init__(self, windowTitle='Genome Atlas Window')
self.connect(self.plotter, QtCore.SIGNAL('CIRCLE_GRAPH_COMPLETE'), self.paintCircleGraph)
self.plotter.plot = 'genomeAtlas'
self.plotter.alignment = alignment
self.plotter.windowsToTopTopologies = windowsToTopTopologies
self.plotter.topologiesToColors = topologiesToColors
self.plotter.windowSize = windowSize
self.plotter.windowOffset = windowOffset
self.plotter.sitesToInformative = sitesToInformative
self.plotter.start()
def __init__(self, data, labels):
Window.__init__(self, windowTitle='TMRCA Graph')
self.plotter.tmrca_graph(data, labels)
self.show()