def do_plotv(session, *args, **kw):
""" Creates a list of plots from the data in ``*args`` and options in
``**kw``, according to the docstring on commands.plot().
"""
sort = kw.get("sort", "none")
sources_list = make_data_sources(session, sort, *args)
plot_type = kw.get("type", "line")
if plot_type == "scatter":
plots = [create_scatter_plot(sources) for sources in sources_list]
elif plot_type == "line":
plots = [create_line_plot(sources) for sources in sources_list]
else:
raise ChacoShellError("Unknown plot type '%s'." % plot_type)
for plot in plots:
plot.orientation = kw.get("orientation", "h")
return plots
def _create_2D_plot(self):
index = 0
secContainer = OverlayPlotContainer(padding = 50, fill_padding = True, bgcolor = "lightgray", use_backbuffer=True)
try:
pcaPoints = []
for batch in self.PCAData.batchs:
if (self.active_scores_combobox == "Post Scores"):
y = [batch.postscores[int(self.Y_PCA)]]
x = [batch.postscores[int(self.X_PCA)]]
else:
x = [batch.prescores[int(self.X_PCA)]]
y = [batch.prescores[int(self.Y_PCA)]]
for i in range(len(x)):
pcaPoints.append((x[i],y[i]))
if (self.Shape == self.phenotypes[0]):
a = 1
elif (self.Shape == self.phenotypes[1]):
a = batch.number
elif (self.Shape == self.phenotypes[2]):
a = batch.type
else:
a = 0
if (self.Color == self.phenotypes[0]):
b = 0
elif(self.Color == self.phenotypes[1]):
b = batch.number
elif(self.Color == self.phenotypes[2]):
b = batch.type
else:
b = 0
tmarker = shapes[a]
bcolor = self.colors[b]
plot = create_scatter_plot((x,y), marker = tmarker, color=getColor(bcolor))
if batch.isSelected:
plot.alpha = 1
else:
plot.fill_alpha = 0.2
plot.bgcolor = "white"
plot.border_visible = True
if index == 0:
value_mapper = plot.value_mapper
index_mapper = plot.index_mapper
add_default_grids(plot)
add_default_axes(plot, vtitle='PCA '+self.Y_PCA, htitle='PCA '+self.X_PCA)
plot.index_range.tight_bounds = False
plot.index_range.refresh()
plot.value_range.tight_bounds = False
plot.value_range.refresh()
plot.tools.append(PanTool(plot))
zoom = ZoomTool(plot, tool_mode="box", always_on=False)
plot.overlays.append(zoom)
dragzoom = DragZoom(plot, drag_button="right")
plot.tools.append(dragzoom)
else:
plot.value_mapper = value_mapper
value_mapper.range.add(plot.value)
plot.index_mapper = index_mapper
index_mapper.range.add(plot.index)
secContainer.add(plot)
index = index +1
lineDraw = LineDrawer2D(plot)
lineDraw.setPCAData(self, self.PCAData)
plot.overlays.append(lineDraw)
self.LeftPlot = secContainer
except ValueError:
pass
def _create_1D1_plot(self):
index = 0
plot0 = Plot(self.plotdata, padding=0)
plot0.padding_left = 5
plot0.padding_bottom = 5
Container = OverlayPlotContainer(padding = 50, fill_padding = True, bgcolor = "lightgray", use_backbuffer=True)
y1 = range(len(self.PCAData.batchs[0].prescores))
points = []
for batch in self.PCAData.batchs:
if (self.active_scores_combobox == "Post Scores"):
x1 = self.PCAData.batchs[index].postscores
else:
x1 = self.PCAData.batchs[index].prescores
if (self.Shape == self.phenotypes[0]):
a = 1
elif (self.Shape == self.phenotypes[1]):
a = batch.number
elif (self.Shape == self.phenotypes[2]):
a = batch.type
else:
a = 0
if (self.Color == self.phenotypes[0]):
b = 0
elif(self.Color == self.phenotypes[1]):
b = batch.number
elif(self.Color == self.phenotypes[2]):
b = batch.type
else:
b = 0
tmarker = shapes[a]
bcolor = self.colors[b]
for i in range(len(x1)):
points.append((x1[i],y1[i]))
plot0 = create_scatter_plot((x1,y1), marker = tmarker, color=getColor(bcolor))
if batch.isSelected:
plot0.alpha = 1
else:
plot0.alpha = 0.2
plot0.bgcolor = "white"
plot0.border_visible = True
if index == 0:
value_mapper = plot0.value_mapper
index_mapper = plot0.index_mapper
add_default_grids(plot0)
add_default_axes(plot0, vtitle='PCA Indices', htitle='PCA Scores')
plot0.index_range.tight_bounds = False
plot0.index_range.refresh()
plot0.value_range.tight_bounds = False
plot0.value_range.refresh()
plot0.tools.append(PanTool(plot0))
zoom = ZoomTool(plot0, tool_mode="box", always_on=False, maintain_aspect_ratio=False)
plot0.overlays.append(zoom)
dragzoom = DragZoom(plot0, drag_button="right", maintain_aspect_ratio=False)
plot0.tools.append(dragzoom)
else:
plot0.value_mapper = value_mapper
value_mapper.range.add(plot0.value)
plot0.index_mapper = index_mapper
index_mapper.range.add(plot0.index)
Container.add(plot0)
index = index +1
self.RightPlot = Container
def _create_2D_plot(self):
index = 0
secContainer = OverlayPlotContainer(padding=50,
fill_padding=True,
bgcolor="lightgray",
use_backbuffer=True)
try:
pcaPoints = []
for batch in self.PCAData.batchs:
if (self.active_scores_combobox == "Post Scores"):
y = [batch.postscores[int(self.Y_PCA)]]
x = [batch.postscores[int(self.X_PCA)]]
else:
x = [batch.prescores[int(self.X_PCA)]]
y = [batch.prescores[int(self.Y_PCA)]]
for i in range(len(x)):
pcaPoints.append((x[i], y[i]))
''' if (self.Shape == self.phenotypes[0]):
a = 1
elif (self.Shape == self.phenotypes[1]):
a = batch.number
elif (self.Shape == self.phenotypes[2]):
a = batch.type
else:
a = 0
if (self.Color == self.phenotypes[0]):
b = 0
elif(self.Color == self.phenotypes[1]):
b = batch.number
elif(self.Color == self.phenotypes[2]):
b = batch.type
else:
b = 0 '''
a = batch.type
b = batch.number
tmarker = shapes[a]
bcolor = self.colors[b]
plot = create_scatter_plot((x, y),
marker=tmarker,
color=getColor(bcolor))
if batch.isSelected:
plot.alpha = 1
else:
plot.alpha = 0.2
plot.bgcolor = "white"
plot.border_visible = True
if index == 0:
value_mapper = plot.value_mapper
index_mapper = plot.index_mapper
add_default_grids(plot)
add_default_axes(plot,
vtitle='PCA ' + self.Y_PCA,
htitle='PCA ' + self.X_PCA)
plot.index_range.tight_bounds = False
plot.index_range.refresh()
plot.value_range.tight_bounds = False
plot.value_range.refresh()
plot.tools.append(PanTool(plot))
zoom = ZoomTool(plot, tool_mode="box", always_on=False)
plot.overlays.append(zoom)
dragzoom = DragZoom(plot, drag_button="right")
plot.tools.append(dragzoom)
else:
plot.value_mapper = value_mapper
value_mapper.range.add(plot.value)
plot.index_mapper = index_mapper
index_mapper.range.add(plot.index)
if batch.isSelected:
secContainer.add(plot)
index = index + 1
lineDraw = LineDrawer2D(plot)
lineDraw.setPCAData(self, self.PCAData)
plot.overlays.append(lineDraw)
self.LeftPlot = secContainer
except ValueError:
pass
def _create_1D1_plot(self):
index = 0
plot0 = Plot(self.plotdata, padding=0)
plot0.padding_left = 5
plot0.padding_bottom = 5
Container = OverlayPlotContainer(padding=50,
fill_padding=True,
bgcolor="lightgray",
use_backbuffer=True)
y1 = range(len(self.PCAData.batchs[0].prescores))
points = []
for batch in self.PCAData.batchs:
if (self.active_scores_combobox == "Post Scores"):
x1 = self.PCAData.batchs[index].postscores
else:
x1 = self.PCAData.batchs[index].prescores
'''if (self.Shape == self.phenotypes[0]):
a = 1
elif (self.Shape == self.phenotypes[1]):
a = batch.number
elif (self.Shape == self.phenotypes[2]):
a = batch.type
else:
a = 0
if (self.Color == self.phenotypes[0]):
b = 0
elif(self.Color == self.phenotypes[1]):
b = batch.number
elif(self.Color == self.phenotypes[2]):
b = batch.type
else:
b = 0 '''
a = batch.type
b = batch.number
tmarker = shapes[a]
bcolor = self.colors[b]
for i in range(len(x1)):
points.append((x1[i], y1[i]))
plot0 = create_scatter_plot((x1, y1),
marker=tmarker,
color=getColor(bcolor))
if batch.isSelected:
plot0.alpha = 1
plot0.alpha = 1
else:
plot0.fill_alpha = 0.2
plot0.edge_alpha = 0.2
plot0.bgcolor = "white"
plot0.border_visible = True
if index == 0:
value_mapper = plot0.value_mapper
index_mapper = plot0.index_mapper
add_default_grids(plot0)
add_default_axes(plot0,
vtitle='PCA Indices',
htitle='PCA Scores')
plot0.index_range.tight_bounds = False
plot0.index_range.refresh()
plot0.value_range.tight_bounds = False
plot0.value_range.refresh()
plot0.tools.append(PanTool(plot0))
zoom = ZoomTool(plot0,
tool_mode="box",
always_on=False,
maintain_aspect_ratio=False)
plot0.overlays.append(zoom)
dragzoom = DragZoom(plot0,
drag_button="right",
maintain_aspect_ratio=False)
plot0.tools.append(dragzoom)
else:
plot0.value_mapper = value_mapper
value_mapper.range.add(plot0.value)
plot0.index_mapper = index_mapper
index_mapper.range.add(plot0.index)
if batch.isSelected:
Container.add(plot0)
index = index + 1
self.RightPlot = Container