class graphManager(wx.Frame):
def __init__(self, parent):
wx.Frame.__init__(self, parent, id=wx.ID_ANY, title=u"ReGenesis", pos=wx.DefaultPosition,
size=wx.Size(MAXWIDTH, MAXHEIGHT),
style=wx.DEFAULT_FRAME_STYLE & ~ (wx.RESIZE_BORDER |
wx.MAXIMIZE_BOX))
self.SetSizeHints(wx.DefaultSize, wx.DefaultSize)
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.renderer = wx.Panel(self, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL)
self.sizer.Add(self.renderer, 1, wx.EXPAND | wx.ALL, 5)
# toolbar
self.toolbar = wx.Panel(self, wx.ID_ANY, wx.DefaultPosition, wx.DefaultSize, wx.TAB_TRAVERSAL)
self.toolbar.SetMinSize(wx.Size(1200, 40))
self.toolbar.SetMaxSize(wx.Size(1200,40))
self.toolbarSizer = wx.BoxSizer(wx.HORIZONTAL)
# adding buttons
self.homeButton = wx.Button(self.toolbar, wx.ID_ANY, u"Reset", wx.DefaultPosition, wx.DefaultSize, 0)
self.toolbarSizer.Add(self.homeButton, 0, wx.ALL, 5)
self.backButton = wx.Button(self.toolbar, wx.ID_ANY, u"Undo", wx.DefaultPosition, wx.DefaultSize, 0)
self.toolbarSizer.Add(self.backButton, 0, wx.ALL, 5)
self.forwardButton = wx.Button(self.toolbar, wx.ID_ANY, u"Redo", wx.DefaultPosition, wx.DefaultSize, 0)
self.toolbarSizer.Add(self.forwardButton, 0, wx.ALL, 5)
self.panButton = wx.Button(self.toolbar, wx.ID_ANY, u"Pan", wx.DefaultPosition, wx.DefaultSize, 0)
self.toolbarSizer.Add(self.panButton, 0, wx.ALL, 5)
self.zoomButton = wx.Button(self.toolbar, wx.ID_ANY, u"Zoom", wx.DefaultPosition, wx.DefaultSize, 0)
self.toolbarSizer.Add(self.zoomButton, 0, wx.ALL, 5)
self.appearanceButton = wx.Button(self.toolbar, wx.ID_ANY, u"Edit Appearance", wx.DefaultPosition, wx.DefaultSize, 0)
self.toolbarSizer.Add(self.appearanceButton, 0, wx.ALL, 5)
self.saveButton = wx.Button(self.toolbar, wx.ID_ANY, u"Save", wx.DefaultPosition, wx.DefaultSize, 0)
self.toolbarSizer.Add(self.saveButton, 0, wx.ALL, 5)
self.loadButton = wx.Button(self.toolbar, wx.ID_ANY, u"Load", wx.DefaultPosition, wx.DefaultSize, 0)
self.toolbarSizer.Add(self.loadButton, 0, wx.ALL, 5)
self.exportButton = wx.Button(self.toolbar, wx.ID_ANY, u"Export", wx.DefaultPosition, wx.DefaultSize, 0)
self.toolbarSizer.Add(self.exportButton, 0, wx.ALL, 5)
self.toolbar.SetSizer(self.toolbarSizer)
self.toolbar.Layout()
self.toolbarSizer.Fit(self.toolbar)
self.sizer.Add(self.toolbar, 1, wx.EXPAND | wx.ALL, 5)
self.SetSizer(self.sizer)
self.Layout()
self.MenuBar = wx.MenuBar(0)
#new graph menu options
self.newGraph = wx.Menu()
self.newPCA = wx.MenuItem(self.newGraph, wx.ID_ANY, u"PCA Graph", wx.EmptyString, wx.ITEM_NORMAL)
self.newGraph.Append(self.newPCA)
self.newAdmixture = wx.MenuItem(self.newGraph, wx.ID_ANY, u"Admixture Graph", wx.EmptyString, wx.ITEM_NORMAL)
self.newGraph.Append(self.newAdmixture)
self.MenuBar.Append(self.newGraph, u"New Graph")
#Manage Graphs Menu
self.manageGraphs = wx.Menu()
self.saveGraph = wx.MenuItem(self.manageGraphs, wx.ID_ANY, u"Save", wx.EmptyString, wx.ITEM_NORMAL)
self.manageGraphs.Append(self.saveGraph)
self.loadGraph = wx.MenuItem(self.manageGraphs, wx.ID_ANY, u"Load", wx.EmptyString, wx.ITEM_NORMAL)
self.manageGraphs.Append(self.loadGraph)
self.exportGraph = wx.MenuItem(self.manageGraphs, wx.ID_ANY, u"Export", wx.EmptyString, wx.ITEM_NORMAL)
self.manageGraphs.Append(self.exportGraph)
self.MenuBar.Append(self.manageGraphs, u"Manage Graphs")
self.SetMenuBar(self.MenuBar)
self.Centre(wx.BOTH)
# Connect Events
# New graph events
self.Bind(wx.EVT_MENU, self.newPCAOnMenuSelection, id=self.newPCA.GetId())
self.Bind(wx.EVT_MENU, self.newAdmixtureOnMenuSelection, id=self.newAdmixture.GetId())
# Manage graph events
self.Bind(wx.EVT_MENU, self.saveGraphOnMenuSelection, id=self.saveGraph.GetId())
self.Bind(wx.EVT_MENU, self.loadGraphOnMenuSelection, id=self.loadGraph.GetId())
self.Bind(wx.EVT_MENU, self.exportGraphOnMenuSelection, id=self.exportGraph.GetId())
# Toolbar Events
self.saveButton.Bind(wx.EVT_BUTTON, self.saveGraphOnMenuSelection)
self.loadButton.Bind(wx.EVT_BUTTON, self.loadGraphOnMenuSelection)
self.exportButton.Bind(wx.EVT_BUTTON, self.onExportButtonClick)
self.zoomButton.Bind(wx.EVT_BUTTON, self.onZoomButtonClick)
self.appearanceButton.Bind(wx.EVT_BUTTON, self.onAppearanceButtonClick)
self.homeButton.Bind(wx.EVT_BUTTON, self.onHomeButtonClick)
self.panButton.Bind(wx.EVT_BUTTON, self.onPanButtonClick)
self.forwardButton.Bind(wx.EVT_BUTTON, self.onForwardButtonClick)
self.backButton.Bind(wx.EVT_BUTTON, self.onBackButtonClick)
# Variable to store which graph type is currently loaded for saving purposes
self.graphType = None
def __del__(self):
pass
def createFigure(self):
"""
Creates figure or clears figure and adds a new subplot to the figure.
"""
# checking if figure exists to avoid reinitializing
if not hasattr(self, 'figure'):
self.figure = mpl.figure.Figure(figsize=(FIGUREWIDTH, FIGUREHEIGHT), dpi=FIGUREDPI)
else:
self.figure.clf()
# add subplot to newly created/cleared figure
self.axes = self.figure.add_subplot(111)
def showGraph(self):
"""
Produces key and canvas.
"""
self.axes.legend()
self.canvas = FigureCanvas(self.renderer, wx.ID_ANY, self.figure)
# Initialises navToolbar instance to use built in functions for custom toolbar
if not hasattr(self, "navToolbar"):
locale = wx.Locale(wx.LANGUAGE_ENGLISH)
self.navToolbar = NavigationToolbar(self.canvas)
self.navToolbar.Hide()
def CreatePCAPlot(self, data):
"""
Creates pca graph and draws it.
"""
self.graph = pcaGraph(data)
pcaData = self.graph.findPcaData(True)
self.plotPcaData(pcaData)
def CreateAdmixturePlot(self, data):
"""
Creates admixture graph and draws it.
"""
self.graph = admixGraph(data)
admixData = self.graph.genDataDictionary()
self.plotAdmixData(admixData)
def plotPcaData(self, pcaData):
"""
Plots PCA data to figure.
"""
pcaAppearance.groupNames = self.graph.getGroups()
pcaAppearance.groupColours = self.graph.getColours()
pcaAppearance.groupShapes = self.graph.getShapes()
pcaAppearance.groupSizes = self.graph.getSize()
pcaAppearance.title = self.graph.getTitle()
pcaAppearance.hasGrid = self.graph.getHasGrid()
pcaAppearance.hasLabels = self.graph.getHasLabels()
self.createFigure()
for group in pcaData:
x = pcaData[group]['x']
y = pcaData[group]['y']
# getting the colours of the groups
colourList = self.graph.getColours()
# getting the shapes of the groups
shapeList = self.graph.getShapes()
#getting the sizes of the groups
sizeList = self.graph.getSize()
#getting the title of the graph
title = self.graph.getTitle()
hasGrid = self.graph.getHasGrid()
hasLabels = self.graph.getHasLabels()
# plotting the graph
self.axes.scatter(x, y, label=group, s=sizeList[group], color=colourList[group], marker=shapeList[group])
self.axes.set_title(title)
if(hasGrid):
self.axes.grid()
if(hasLabels):
self.axes.set_xlabel(self.graph.getXLabel())
self.axes.set_ylabel(self.graph.getYLabel())
self.showGraph()
return
def plotAdmixData(self, admixData):
"""
Plots admixture data to figure.
"""
groups = list(admixData.keys())
ancestryLabels = list(admixData[groups[0]].keys())
individualCount = 0
groupCenters = []
# creating figure
self.createFigure()
fullRatios = []
self.axes.set_xticklabels([])
for group in admixData:
ratios = []
for ancestry in admixData[group]:
anc = admixData[group][ancestry]
ratios.append(anc)
numAncestries = len(ratios)
numIndividuals = len(ratios[0])
# Normalising ratios so they add up to 1
tempRatios = list(zip(*ratios))
sums = list(map(sum, tempRatios))
for ancestry in ratios:
for i in range(len(ancestry)):
ancestry[i] /= sums[i]
# storing values used for separating groups at presentation
groupCenters.append(individualCount + (numIndividuals/2))
individualCount += numIndividuals
self.axes.axvline(individualCount, color='w')
if len(fullRatios) > 0:
for i in range(len(fullRatios)):
fullRatios[i].extend(ratios[i])
else:
fullRatios = ratios
# plotting bars
indexes = [i for i in range(individualCount)]
self.axes.bar(indexes, fullRatios[0], 1, label=ancestryLabels[0])
# barBottom keeps track of the current height of each bar so subsequent bars can be plotted above
barBottom = [0 for i in range(individualCount)]
for i in range(0, numAncestries - 1):
# increasing height of barBottom
barBottom = [x + y for x, y in zip(barBottom, fullRatios[i])]
self.axes.bar(indexes, fullRatios[i + 1], 1, bottom=barBottom, label=ancestryLabels[i + 1])
# setting labels for better readability
self.axes.set_xticks(groupCenters)
self.axes.set_xticklabels(groups)
self.showGraph()
# Event Handlers
def newPCAOnMenuSelection(self, event):
"""
Event handler for new PCA menu selection.
"""
self.child = pcaCreator(self)
self.Disable()
self.child.ShowModal()
if self.child.result == "CANCEL":
event.Skip()
elif self.child.result == "CONFIRM":
self.CreatePCAPlot(self.child._dataDict)
def newAdmixtureOnMenuSelection(self, event):
"""
Event handler for new Admixture menu selection.
"""
self.child = admixCreator(self)
self.Disable()
self.child.ShowModal()
if self.child.result == "CANCEL":
event.Skip()
elif self.child.result == "CONFIRM":
self.CreateAdmixturePlot(self.child._dataDict)
def saveGraphOnMenuSelection(self, event):
"""
Event handler for save Graph menu selection.
"""
with wx.FileDialog(self, "Save Graph file", wildcard="Regenesis Graph File files (*.rgf)|*.rgf",
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) as fileDialog:
if fileDialog.ShowModal() == wx.ID_CANCEL:
return # the user changed their mind
# save the current contents in the file
pathname = fileDialog.GetPath()
try:
with open(pathname, 'w', encoding='utf-8') as file:
self.doSaveData(file)
except IOError:
wx.LogError("Cannot save current data in file '%s'." % pathname)
def doSaveData(self, f):
"""
Saves project state to file.
"""
# find dictionary of values to plot
if self.graph.getGraphType() == 'admix':
data = self.graph.getSaveFileData()
# Add a graph type key to the data dict
data.update({"GraphType" : 'admix'})
elif self.graph.getGraphType() == 'pca':
data = self.graph.getSaveFileData()
# Add a graph type key to the data dict
data.update({"GraphType" : "pca"})
json.dump(data, f, ensure_ascii=False)
f.close()
def loadGraphOnMenuSelection(self, event):
"""
Event handler for load Graph menu selection.
"""
# otherwise ask the user what new file to open
with wx.FileDialog(self, "Load Graph file", wildcard="Regenesis Graph File files (*.rgf)|*.rgf",
style=wx.FD_OPEN | wx.FD_FILE_MUST_EXIST) as fileDialog:
if fileDialog.ShowModal() == wx.ID_CANCEL:
return # the user changed their mind
# Proceed loading the file chosen by the user
pathname = fileDialog.GetPath()
try:
with open(pathname, 'r') as file:
self.doLoadData(file)
except IOError:
wx.LogError("Cannot open file '%s'." % file)
def doLoadData(self,f):
"""
Loads project state from file.
"""
data = json.load(f)
if data.get("GraphType") == 'admix':
# Delete the Graph Type key from the data dict
del data["GraphType"]
self.CreateAdmixturePlot(data)
elif data.get("GraphType") == 'pca':
# Delete the Graph Type key from the data dict
del data["GraphType"]
self.CreatePCAPlot(data)
f.close()
def exportGraphOnMenuSelection(self, event):
"""
Exports graph as image.
"""
self.navToolbar.save_figure()
def onZoomButtonClick(self, event):
"""
Activates zoom mode on graph.
"""
self.navToolbar.zoom()
def onAppearanceButtonClick(self, event):
"""
Opens appearance editor.
"""
if self.graph.getGraphType() == 'pca':
self.child = pcaAppearance(self)
self.Disable()
self.child.ShowModal()
else:
msgDlg = wx.MessageDialog(parent=self, message="Appearance editing functionality for admixture graph still to come in future releases",
caption="Edit Admixture graph appearance", style=wx.ICON_INFORMATION)
val = msgDlg.ShowModal()
msgDlg.Show()
if self.child.result == "CANCEL":
event.Skip()
elif self.child.result == "CONFIRM":
if self.graph.getGraphType() == 'pca':
#re-plotting the graph with the newly chosen colours
newColours = self.child.GetColours()
self.graph.setColours(newColours)
#re-plotting the graph with the newly chosen shape
newShapes = self.child.GetShapes()
self.graph.setShapes(newShapes)
#re-plotting the graph with the new group size
newSize = self.child.GetSize()
self.graph.setSize(newSize)
#re-plotting graph with new title
newTitle = self.child.GetTitle()
self.graph.setTitle(newTitle)
#re-plotting graph with grid settings
grid = self.child.GetHasGrid()
self.graph.setHasGrid(grid)
#re-plotting graph with labels settings
labels = self.child.GetHasLabels()
self.graph.setHasLabels(labels)
pcaData = self.graph.findPcaData(False)
self.plotPcaData(pcaData)
#self.CreatePCAPlot(self.child._dataDict)
elif self.graph.getGraphType() == "admix":
wx.MessageDialog(None, "Admixture Appearance editing to b")
def onHomeButtonClick(self, event):
"""
Resets graph panning and zooming
"""
self.navToolbar.home()
def onPanButtonClick(self, event):
"""
Activates Pan mode on graph.
"""
self.navToolbar.pan()
def onConfigureButtonClick(self, event):
self.navToolbar.configure_subplots()
def onBackButtonClick(self, event):
"""
Undoes latest panning or zooming change.
"""
self.navToolbar.back()
def onForwardButtonClick(self, event):
"""
Redoes latest undone panning or zooming change.
"""
self.navToolbar.forward()
def onExportButtonClick(self, event):
"""
Exports graph as image.
"""
self.navToolbar.save_figure()
