class wishbone_gui(tk.Tk):
def __init__(self,parent):
tk.Tk.__init__(self,parent)
self.parent = parent
self.initialize()
def initialize(self):
self.grid()
self.vals = None
self.currentPlot = None
#set up menu bar
self.menubar = tk.Menu(self)
self.fileMenu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="File", menu=self.fileMenu)
self.fileMenu.add_command(label="Load data", command=self.loadData)
self.fileMenu.add_command(label="Save data", state='disabled', command=self.saveData)
self.fileMenu.add_command(label="Exit Wishbone", command=self.quitWB)
self.analysisMenu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="Analysis", menu=self.analysisMenu)
self.analysisMenu.add_command(label="Principal component analysis", state='disabled', command=self.runPCA)
self.analysisMenu.add_command(label="tSNE", state='disabled', command=self.runTSNE)
self.analysisMenu.add_command(label="Diffusion map", state='disabled', command=self.runDM)
self.analysisMenu.add_command(label="GSEA", state='disabled', command=self.runGSEA)
self.analysisMenu.add_command(label="Wishbone", state='disabled', command=self.runWishbone)
self.visMenu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="Visualization", menu=self.visMenu)
self.visMenu.add_command(label="Principal component analysis", state='disabled', command=self.plotPCA)
self.visMenu.add_command(label="tSNE", state='disabled', command=self.plotTSNE)
self.visMenu.add_command(label="Diffusion map", state='disabled', command=self.plotDM)
self.visMenu.add_command(label="GSEA Results", state='disabled', command=self.showGSEAResults)
self.wishboneMenu = tk.Menu(self)
self.visMenu.add_cascade(label="Wishbone", menu=self.wishboneMenu)
self.wishboneMenu.add_command(label="On tSNE", state='disabled', command=self.plotWBOnTsne)
self.wishboneMenu.add_command(label="Marker trajectory", state='disabled', command=self.plotWBMarkerTrajectory)
self.wishboneMenu.add_command(label="Heat map", state='disabled', command=self.plotWBHeatMap)
self.visMenu.add_command(label="Gene expression", state='disabled', command=self.plotGeneExpOntSNE)
self.visMenu.add_command(label="Set gate", state='disabled', command=self.setGate)
self.config(menu=self.menubar)
#intro screen
tk.Label(self, text=u"Wishbone", font=('Helvetica', 48), fg="black", bg="white", padx=100, pady=50).grid(row=0)
tk.Label(self, text=u"To get started, select a data file by clicking File > Load Data", fg="black", bg="white", padx=100, pady=25).grid(row=1)
#update
self.protocol('WM_DELETE_WINDOW', self.quitWB)
self.grid_columnconfigure(0,weight=1)
self.resizable(True,True)
self.update()
self.geometry(self.geometry())
self.focus_force()
def loadData(self):
self.dataFileName = filedialog.askopenfilename(title='Load data file', initialdir='~/.wishbone/data')
if(self.dataFileName != ""):
#pop up data options menu
self.fileInfo = tk.Toplevel()
self.fileInfo.title("Data options")
tk.Label(self.fileInfo, text=u"File name: ").grid(column=0, row=0)
tk.Label(self.fileInfo, text=self.dataFileName.split('/')[-1]).grid(column=1, row=0)
tk.Label(self.fileInfo,text=u"Name:" ,fg="black",bg="white").grid(column=0, row=1)
self.fileNameEntryVar = tk.StringVar()
tk.Entry(self.fileInfo, textvariable=self.fileNameEntryVar).grid(column=1,row=1)
if self.dataFileName.split('.')[len(self.dataFileName.split('.'))-1] == 'fcs':
tk.Label(self.fileInfo,text=u"Cofactor:" ,fg="black",bg="white").grid(column=0, row=2)
self.cofactorVar = tk.IntVar()
self.cofactorVar.set(5)
tk.Entry(self.fileInfo, textvariable=self.cofactorVar).grid(column=1,row=2)
elif self.dataFileName.split('.')[len(self.dataFileName.split('.'))-1] == 'csv':
self.normalizeVar = tk.BooleanVar()
tk.Checkbutton(self.fileInfo, text=u"Normalize", variable=self.normalizeVar).grid(column=0, row=2, columnspan=2)
tk.Label(self.fileInfo, text=u"The normalize parameter is used for correcting for library size among cells.").grid(column=0, row=3, columnspan=2)
tk.Button(self.fileInfo, text="Cancel", command=self.fileInfo.destroy).grid(column=0, row=4)
tk.Button(self.fileInfo, text="Load", command=self.processData).grid(column=1, row=4)
self.wait_window(self.fileInfo)
def processData(self):
#clear intro screen
for item in self.grid_slaves():
item.grid_forget()
#display file name
tk.Label(self,text=u"File name: " + self.fileNameEntryVar.get(), fg="black",bg="white").grid(column=0,row=0)
#set up canvas for plots
self.fig, self.ax = wishbone.wb.get_fig()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='NSEW')
tk.Label(self, text=u"Visualizations:", fg='black', bg='white').grid(column=0, row=1)
#load data based on input type
if self.dataFileName.split('.')[len(self.dataFileName.split('.'))-1] == 'fcs': # mass cytometry data
self.scdata = wishbone.wb.SCData.from_fcs(os.path.expanduser(self.dataFileName),
cofactor=self.cofactorVar.get())
self.wb = None
elif self.dataFileName.split('.')[len(self.dataFileName.split('.'))-1] == 'csv': # sc-seq data
self.scdata = wishbone.wb.SCData.from_csv(os.path.expanduser(self.dataFileName), data_type='sc-seq',
normalize=self.normalizeVar.get())
self.wb = None
else:
self.wb = wishbone.wb.Wishbone.load(self.dataFileName)
self.scdata = self.wb.scdata
#set up buttons based on data type
if self.scdata.data_type == 'sc-seq':
self.PCAButton = tk.Button(self, text=u"PCA", state='disabled', command=self.plotPCA)
self.PCAButton.grid(column=0, row=2)
self.tSNEButton = tk.Button(self, text=u"tSNE", state='disabled', command=self.plotTSNE)
self.tSNEButton.grid(column=0, row=3)
self.DMButton = tk.Button(self, text=u"Diffusion map", state='disabled', command=self.plotDM)
self.DMButton.grid(column=0, row=4)
self.GSEAButton = tk.Button(self, text=u"GSEA Results", state='disabled', command=self.showGSEAResults)
self.GSEAButton.grid(column=0, row=5)
self.WBButton = tk.Button(self, text=u"Wishbone", state='disabled', command=self.plotWBOnTsne)
self.WBButton.grid(column=0, row=6)
self.geneExpButton = tk.Button(self, text=u"Gene expression", state='disabled', command=self.plotGeneExpOntSNE)
self.geneExpButton.grid(column=0, row=7)
self.setGateButton = tk.Button(self, text=u"Set gate", state='disabled', command=self.setGate)
self.setGateButton.grid(column=0, row=8)
self.saveButton = tk.Button(self, text=u"Save plot", state='disabled', command=self.savePlot)
self.saveButton.grid(column = 4, row=0)
self.diff_component = tk.StringVar()
self.diff_component.set('Component 1')
self.component_menu = tk.OptionMenu(self, self.diff_component,
'Component 1', 'Component 2', 'Component 3',
'Component 4', 'Component 5', 'Component 6',
'Component 7', 'Component 8', 'Component 9')
self.component_menu.config(state='disabled')
self.component_menu.grid(row=0, column=2)
self.updateButton = tk.Button(self, text=u"Update component", command=self.updateComponent, state='disabled')
self.updateButton.grid(column=3, row=0)
#enable buttons based on current state of scdata object
if self.scdata.pca:
self.analysisMenu.entryconfig(1, state='normal')
self.visMenu.entryconfig(0, state='normal')
self.PCAButton.config(state='normal')
if isinstance(self.scdata.tsne, pd.DataFrame):
self.analysisMenu.entryconfig(2, state='normal')
self.visMenu.entryconfig(1, state='normal')
self.visMenu.entryconfig(5, state='normal')
self.tSNEButton.config(state='normal')
self.geneExpButton.config(state='normal')
if isinstance(self.scdata.diffusion_eigenvectors, pd.DataFrame):
self.analysisMenu.entryconfig(3, state='normal')
self.analysisMenu.entryconfig(4, state='normal')
self.visMenu.entryconfig(2, state='normal')
self.DMButton.config(state='normal')
else:
self.tSNEButton = tk.Button(self, text=u"tSNE", state='disabled', command=self.plotTSNE)
self.tSNEButton.grid(column=0, row=2)
self.DMButton = tk.Button(self, text=u"Diffusion map", state='disabled', command=self.plotDM)
self.DMButton.grid(column=0, row=3)
self.WBButton = tk.Button(self, text=u"Wishbone", state='disabled', command=self.plotWBOnTsne)
self.WBButton.grid(column=0, row=4)
self.geneExpButton = tk.Button(self, text=u"Gene expression", state='disabled', command=self.plotGeneExpOntSNE)
self.geneExpButton.grid(column=0, row=5)
self.setGateButton = tk.Button(self, text=u"Set gate", state='disabled', command=self.setGate)
self.setGateButton.grid(column=0, row=6)
self.saveButton = tk.Button(self, text=u"Save plot", state='disabled', command=self.savePlot)
self.saveButton.grid(column = 4, row=0)
self.analysisMenu.delete(0)
self.analysisMenu.delete(2)
self.visMenu.delete(0)
self.visMenu.delete(2)
self.analysisMenu.entryconfig(1, state='normal')
#enable buttons based on current state of scdata object
if isinstance(self.scdata.tsne, pd.DataFrame):
self.visMenu.entryconfig(0, state='normal')
self.visMenu.entryconfig(3, state='normal')
self.tSNEButton.config(state='normal')
self.geneExpButton.config(state='normal')
if isinstance(self.scdata.diffusion_eigenvectors, pd.DataFrame):
self.analysisMenu.entryconfig(2, state='normal')
self.visMenu.entryconfig(1, state='normal')
self.DMButton.config(state='normal')
#enable buttons
self.analysisMenu.entryconfig(0, state='normal')
self.fileMenu.entryconfig(1, state='normal')
if self.wb:
if isinstance(self.wb.trajectory, pd.Series):
self.wishboneMenu.entryconfig(0, state='normal')
self.wishboneMenu.entryconfig(1, state='normal')
self.wishboneMenu.entryconfig(2, state='normal')
self.WBButton.config(state='normal')
#get genes
self.genes = self.scdata.data.columns.values
self.gates = {}
self.geometry('800x550')
#destroy pop up menu
self.fileInfo.destroy()
def saveData(self):
pickleFileName = filedialog.asksaveasfilename(title='Save Wishbone Data', defaultextension='.p', initialfile=self.fileNameEntryVar.get())
if pickleFileName != None:
if self.wb != None:
self.wb.save(pickleFileName)
else:
self.scdata.save_as_wishbone(pickleFileName)
def runPCA(self):
self.scdata.run_pca()
#enable buttons
self.analysisMenu.entryconfig(1, state='normal')
self.visMenu.entryconfig(0, state='normal')
self.PCAButton.config(state='normal')
def runTSNE(self):
#pop up for # components
self.tsneOptions = tk.Toplevel()
self.tsneOptions.title("tSNE options")
if self.scdata.data_type == 'sc-seq':
tk.Label(self.tsneOptions,text=u"Number of components:" ,fg="black",bg="white").grid(column=0, row=0)
self.nCompVar = tk.IntVar()
self.nCompVar.set(15)
tk.Entry(self.tsneOptions, textvariable=self.nCompVar).grid(column=1,row=0)
tk.Label(self.tsneOptions,text=u"Perplexity:" ,fg="black",bg="white").grid(column=0, row=1)
self.perplexityVar = tk.IntVar()
self.perplexityVar.set(30)
tk.Entry(self.tsneOptions, textvariable=self.perplexityVar).grid(column=1,row=1)
tk.Button(self.tsneOptions, text="Run", command=self._runTSNE).grid(column=1, row=2)
tk.Button(self.tsneOptions, text="Cancel", command=self.tsneOptions.destroy).grid(column=0, row=2)
self.wait_window(self.tsneOptions)
def _runTSNE(self):
if self.scdata.data_type == 'sc-seq':
self.scdata.run_tsne(n_components=self.nCompVar.get(), perplexity=self.perplexityVar.get())
else:
self.scdata.run_tsne(n_components=None, perplexity=self.perplexityVar.get())
self.gates = {}
#enable buttons
if self.scdata.data_type == 'sc-seq':
self.analysisMenu.entryconfig(2, state='normal')
self.visMenu.entryconfig(1, state='normal')
self.visMenu.entryconfig(5, state='normal')
else:
self.visMenu.entryconfig(0, state='normal')
self.visMenu.entryconfig(3, state='normal')
self.tSNEButton.config(state='normal')
self.geneExpButton.config(state='normal')
self.tsneOptions.destroy()
def runDM(self):
self.scdata.run_diffusion_map()
#enable buttons
if self.scdata.data_type == 'sc-seq':
self.analysisMenu.entryconfig(3, state='normal')
self.analysisMenu.entryconfig(4, state='normal')
self.visMenu.entryconfig(2, state='normal')
else:
self.analysisMenu.entryconfig(2, state='normal')
self.visMenu.entryconfig(1, state='normal')
self.DMButton.config(state='normal')
def runGSEA(self):
self.GSEAFileName = filedialog.askopenfilename(title='Select gmt File', initialdir='~/.wishbone/tools')
if self.GSEAFileName != "":
self.scdata.run_diffusion_map_correlations()
self.scdata.data.columns = self.scdata.data.columns.str.upper()
self.outputPrefix = filedialog.asksaveasfilename(title='Input file prefix for saving output', initialdir='~/.wishbone/gsea')
if 'mouse' in self.GSEAFileName:
gmt_file_type = 'mouse'
else:
gmt_file_type = 'human'
self.reports = self.scdata.run_gsea(output_stem= os.path.expanduser(self.outputPrefix),
gmt_file=(gmt_file_type, self.GSEAFileName.split('/')[-1]))
#enable buttons
self.visMenu.entryconfig(3, state='normal')
self.GSEAButton.config(state='normal')
def runWishbone(self):
#popup menu for wishbone options
self.wbOptions = tk.Toplevel()
self.wbOptions.title("Wishbone Options")
#s
tk.Label(self.wbOptions,text=u"Start cell:",fg="black",bg="white").grid(column=0,row=0)
self.start = tk.StringVar()
tk.Entry(self.wbOptions, textvariable=self.start).grid(column=1,row=0)
if(len(self.gates) > 0):
self.cell_gate = tk.StringVar()
self.cell_gate.set('Use cell gate')
self.gate_menu = tk.OptionMenu(self.wbOptions, self.cell_gate,
*list(self.gates.keys()))
self.gate_menu.grid(row=0, column=2)
#k
tk.Label(self.wbOptions,text=u"k:",fg="black",bg="white").grid(column=0,row=1)
self.k = tk.IntVar()
tk.Entry(self.wbOptions, textvariable=self.k).grid(column=1,row=1)
self.k.set(15)
#components list
tk.Label(self.wbOptions, text=u"Components list:", fg='black', bg='white').grid(column=0, row=2)
self.compList = tk.StringVar()
tk.Entry(self.wbOptions, textvariable=self.compList).grid(column=1, row=2)
self.compList.set("1, 2, 3")
#num waypoints
tk.Label(self.wbOptions, text=u"Number of waypoints:", fg='black', bg='white').grid(column=0, row=3)
self.numWaypoints = tk.IntVar()
tk.Entry(self.wbOptions, textvariable=self.numWaypoints).grid(column=1, row=3)
self.numWaypoints.set(250)
#branch
self.branch = tk.BooleanVar()
self.branch.set(True)
tk.Checkbutton(self.wbOptions, text=u"Branch", variable=self.branch).grid(column=0, row=4, columnspan=2)
tk.Button(self.wbOptions, text="Run", command=self._runWishbone).grid(column=1, row=5)
tk.Button(self.wbOptions, text="Cancel", command=self.wbOptions.destroy).grid(column=0, row=5)
self.wait_window(self.wbOptions)
def _runWishbone(self):
self.wb = wishbone.wb.Wishbone(self.scdata)
if self.cell_gate.get() == 'Use cell gate':
self.wb.run_wishbone(start_cell=self.start.get(), k=self.k.get(), components_list=[int(comp) for comp in self.compList.get().split(',')], num_waypoints=self.numWaypoints.get())
else:
#randomly select start cell in gate
print('Using cell gate:')
print(self.cell_gate.get())
start_cell = random.sample(list(self.gates[self.cell_gate.get()]), 1)[0]
print(start_cell)
self.wb.run_wishbone(start_cell=start_cell, k=self.k.get(), components_list=[int(comp) for comp in self.compList.get().split(',')], num_waypoints=self.numWaypoints.get())
#enable buttons
self.wishboneMenu.entryconfig(0, state='normal')
self.wishboneMenu.entryconfig(1, state='normal')
self.wishboneMenu.entryconfig(2, state='normal')
self.WBButton.config(state='normal')
self.wbOptions.destroy()
def plotPCA(self):
self.saveButton.config(state='normal')
self.setGateButton.config(state='disabled')
if self.scdata.data_type == 'sc-seq':
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')
else:
self.visMenu.entryconfig(4, state='disabled')
#pop up for # components
self.PCAOptions = tk.Toplevel()
self.PCAOptions.title("PCA Plot Options")
tk.Label(self.PCAOptions,text=u"Max variance explained (ylim):",fg="black",bg="white").grid(column=0, row=0)
self.yLimVar = tk.DoubleVar()
self.yLimVar.set(round(self.scdata.pca['eigenvalues'][0][0], 2))
tk.Entry(self.PCAOptions, textvariable=self.yLimVar).grid(column=1,row=0)
tk.Label(self.PCAOptions, text=u"Number of components:", fg='black', bg='white').grid(column=0, row=1)
self.compVar = tk.IntVar()
self.compVar.set(15)
tk.Entry(self.PCAOptions, textvariable=self.compVar).grid(column=1, row=1)
tk.Button(self.PCAOptions, text="Plot", command=self._plotPCA).grid(column=1, row=2)
tk.Button(self.PCAOptions, text="Cancel", command=self.PCAOptions.destroy).grid(column=0, row=2)
self.wait_window(self.PCAOptions)
def _plotPCA(self):
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_pca_variance_explained(ylim=(0, self.yLimVar.get()), n_components=self.compVar.get())
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='NW')
self.currentPlot = 'pca'
#enable buttons
self.saveButton.config(state='normal')
self.PCAOptions.destroy()
def plotTSNE(self):
self.saveButton.config(state='normal')
self.setGateButton.config(state='normal')
if self.scdata.data_type == 'sc-seq':
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='normal')
else:
self.visMenu.entryconfig(4, state='normal')
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_tsne()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='NW')
self.currentPlot = 'tsne'
def plotDM(self):
self.saveButton.config(state='normal')
self.setGateButton.config(state='disabled')
if self.scdata.data_type == 'sc-seq':
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')
else:
self.visMenu.entryconfig(4, state='disabled')
self.geometry('950x550')
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_diffusion_components()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='W')
self.currentPlot = 'dm_components'
def showGSEAResults(self):
self.saveButton.config(state='disabled')
self.component_menu.config(state='normal')
self.updateButton.config(state='normal')
self.setGateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')
self.resetCanvas()
self.canvas = tk.Canvas(self, width=600, height=300)
self.canvas.grid(column=1, row=1, rowspan=17, columnspan=4)
self.outputText(1)
self.currentPlot = 'GSEA_result_'+self.diff_component.get()
def updateComponent(self):
self.resetCanvas()
self.canvas = tk.Canvas(self, width=600, height=300)
self.canvas.grid(column=1, row=1, rowspan=17, columnspan=4,sticky='NSEW')
self.outputText(int(self.diff_component.get().split(' ')[-1]))
self.currentPlot = 'GSEA_result_'+self.diff_component.get()
def outputText(self, diff_component):
pos_text = str(self.reports[diff_component]['pos']).split('\n')
pos_text = pos_text[1:len(pos_text)-1]
pos_text = '\n'.join(pos_text)
neg_text = str(self.reports[diff_component]['neg']).split('\n')
neg_text = neg_text[1:len(neg_text)-1]
neg_text = '\n'.join(neg_text)
self.canvas.create_text(5, 5, anchor='nw', text='Positive correlations:\n\n', font=('Helvetica', 16, 'bold'))
self.canvas.create_text(5, 50, anchor='nw', text=pos_text)
self.canvas.create_text(5, 150, anchor='nw', text='Negative correlations:\n\n', font=('Helvetica', 16, 'bold'))
self.canvas.create_text(5, 200, anchor='nw', text=neg_text)
def plotWBOnTsne(self):
self.saveButton.config(state='normal')
self.setGateButton.config(state='disabled')
if self.scdata.data_type == 'sc-seq':
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')
else:
self.visMenu.entryconfig(4, state='disabled')
self.resetCanvas()
self.fig, self.ax = self.wb.plot_wishbone_on_tsne()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4)
self.currentPlot = 'wishbone_on_tsne'
def plotWBMarkerTrajectory(self):
self.getGeneSelection()
if len(self.selectedGenes) < 1:
print('Error: must select at least one gene')
else:
self.saveButton.config(state='normal')
self.setGateButton.config(state='disabled')
if self.scdata.data_type == 'sc-seq':
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')
else:
self.visMenu.entryconfig(4, state='disabled')
self.resetCanvas()
self.vals, self.fig, self.ax = self.wb.plot_marker_trajectory(self.selectedGenes)
self.fig.set_size_inches(10, 4, forward=True)
self.fig.tight_layout()
self.fig.subplots_adjust(right=0.8)
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=5, sticky='W')
self.currentPlot = 'wishbone_marker_trajectory'
self.geometry('1050x550')
#enable buttons
self.wishboneMenu.entryconfig(2, state='normal')
def plotWBHeatMap(self):
self.getGeneSelection()
if len(self.selectedGenes) < 1:
print('Error: must select at least one gene')
else:
self.saveButton.config(state='normal')
self.setGateButton.config(state='disabled')
if self.scdata.data_type == 'sc-seq':
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')
else:
self.visMenu.entryconfig(4, state='disabled')
self.resetCanvas()
self.vals, self.fig, self.ax = self.wb.plot_marker_trajectory(self.selectedGenes)
self.fig, self.ax = self.wb.plot_marker_heatmap(self.vals)
self.fig.set_size_inches(10, 4, forward=True)
self.fig.tight_layout()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=5, sticky='W')
self.currentPlot = 'wishbone_marker_heatmap'
def plotGeneExpOntSNE(self):
self.getGeneSelection()
if len(self.selectedGenes) < 1:
print('Error: must select at least one gene')
else:
self.saveButton.config(state='normal')
self.setGateButton.config(state='disabled')
if self.scdata.data_type == 'sc-seq':
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')
else:
self.visMenu.entryconfig(4, state='disabled')
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_gene_expression(self.selectedGenes)
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='W')
self.currentPlot = 'gene_expression_tsne'
self.geometry('950x550')
def getGeneSelection(self):
#popup menu to get selected genes
self.geneSelection = tk.Toplevel()
self.geneSelection.title("Select Genes")
tk.Label(self.geneSelection,text=u"Genes:",fg="black",bg="white").grid(row=0)
self.geneInput = wishbone.autocomplete_entry.AutocompleteEntry(self.genes.tolist(), self.geneSelection, listboxLength=6)
self.geneInput.grid(row=1)
self.geneInput.bind('<Return>', self.AddToSelected)
self.geneSelectBox = tk.Listbox(self.geneSelection, selectmode=tk.EXTENDED)
self.geneSelectBox.grid(row=2, rowspan=10)
self.geneSelectBox.bind('<BackSpace>', self.DeleteSelected)
self.selectedGenes = []
tk.Button(self.geneSelection, text="Use selected genes", command=self.geneSelection.destroy).grid(row=12)
tk.Button(self.geneSelection, text="Cancel", command=self.cancelGeneSelection).grid(row=13)
self.wait_window(self.geneSelection)
def cancelGeneSelection(self):
self.selectedGenes = []
self.geneSelection.destroy()
def AddToSelected(self, event):
self.selectedGenes.append(self.geneInput.get())
self.geneSelectBox.insert(tk.END, self.selectedGenes[len(self.selectedGenes)-1])
def DeleteSelected(self, event):
selected = self.geneSelectBox.curselection()
pos = 0
for i in selected:
idx = int(i) - pos
self.geneSelectBox.delete( idx,idx )
self.selectedGenes = self.selectedGenes[:idx] + self.selectedGenes[idx+1:]
pos = pos + 1
def savePlot(self):
self.plotFileName = filedialog.asksaveasfilename(title='Save Plot', defaultextension='.png', initialfile=self.fileNameEntryVar.get()+"_"+self.currentPlot)
if self.plotFileName != None:
self.fig.savefig(self.plotFileName)
def setGate(self):
#pop up for gate name
self.gateOptions = tk.Toplevel()
self.gateOptions.title("Create gate for start cells")
tk.Label(self.gateOptions,text=u"Gate name:" ,fg="black",bg="white").grid(column=0, row=0)
self.gateName = tk.StringVar()
self.gateName.set('Gate ' + str(len(self.gates) + 1))
tk.Entry(self.gateOptions, textvariable=self.gateName).grid(column=1,row=0)
tk.Button(self.gateOptions, text="Select gate", command=self._setGate).grid(column=1, row=1)
tk.Button(self.gateOptions, text="Cancel", command=self.gateOptions.destroy).grid(column=0, row=1)
self.wait_window(self.gateOptions)
def _setGate(self):
self.gateOptions.destroy()
self.buttonPress = self.canvas.mpl_connect('button_press_event', self._startGate)
self.buttonRelease = self.canvas.mpl_connect('button_release_event', self._endGate)
self.canvas.get_tk_widget().config(cursor='plus')
def _startGate(self, event):
self.start_x = event.xdata
self.start_y = event.ydata
def _endGate(self, event):
#draw gate rectangle
start_x = self.start_x if self.start_x < event.xdata else event.xdata
start_y = self.start_y if self.start_y < event.ydata else event.ydata
width = np.absolute(event.xdata-self.start_x)
height = np.absolute(event.ydata-self.start_y)
rect = Rectangle((start_x, start_y), width, height,
fill=False, ec='black', alpha=1, lw=2)
self.ax.add_patch(rect)
self.canvas.draw()
#disable mouse events
self.canvas.mpl_disconnect(self.buttonPress)
self.canvas.mpl_disconnect(self.buttonRelease)
self.canvas.get_tk_widget().config(cursor='arrow')
#save cell gate
gate = Path([[start_x, start_y],
[start_x + width, start_y],
[start_x + width, start_y + height],
[start_x, start_y + height],
[start_x, start_y]])
gated_cells = self.scdata.tsne.index[gate.contains_points(self.scdata.tsne)]
self.gates[self.gateName.get()] = gated_cells
#replot tSNE w gate colored
self.fig.clf()
plt.scatter(self.scdata.tsne['x'], self.scdata.tsne['y'], s=10, edgecolors='none', color='lightgrey')
plt.scatter(self.scdata.tsne.ix[gated_cells, 'x'], self.scdata.tsne.ix[gated_cells, 'y'], s=10, edgecolors='none')
self.canvas.draw()
self.setGateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')
def resetCanvas(self):
self.fig.clf()
if type(self.canvas) is FigureCanvasTkAgg:
for item in self.canvas.get_tk_widget().find_all():
self.canvas.get_tk_widget().delete(item)
else:
for item in self.canvas.find_all():
self.canvas.delete(item)
def quitWB(self):
self.quit()
self.destroy()
class wishbone_gui(tk.Tk):
def __init__(self,parent):
tk.Tk.__init__(self,parent)
self.parent = parent
self.initialize()
def initialize(self):
self.grid()
self.vals = None
self.currentPlot = None
#set up menu bar
self.menubar = tk.Menu(self)
self.fileMenu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="File", menu=self.fileMenu)
self.fileMenu.add_command(label="Load data", command=self.loadData)
self.fileMenu.add_command(label="Exit Wishbone", command=self.quitWB)
self.analysisMenu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="Analysis", menu=self.analysisMenu)
self.analysisMenu.add_command(label="Principal component analysis", state='disabled', command=self.runPCA)
self.analysisMenu.add_command(label="tSNE", state='disabled', command=self.runTSNE)
self.analysisMenu.add_command(label="Diffusion map", state='disabled', command=self.runDM)
self.analysisMenu.add_command(label="GSEA", state='disabled', command=self.runGSEA)
self.analysisMenu.add_command(label="Wishbone", state='disabled', command=self.runWishbone)
self.visMenu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="Visualization", menu=self.visMenu)
self.visMenu.add_command(label="Principal component analysis", state='disabled', command=self.plotPCA)
self.visMenu.add_command(label="tSNE", state='disabled', command=self.plotTSNE)
self.visMenu.add_command(label="Diffusion map", state='disabled', command=self.plotDM)
self.visMenu.add_command(label="GSEA Results", state='disabled', command=self.showGSEAResults)
self.wishboneMenu = tk.Menu(self)
self.visMenu.add_cascade(label="Wishbone", menu=self.wishboneMenu)
self.wishboneMenu.add_command(label="On tSNE", state='disabled', command=self.plotWBOnTsne)
self.wishboneMenu.add_command(label="Marker trajectory", state='disabled', command=self.plotWBMarkerTrajectory)
self.wishboneMenu.add_command(label="Heat map", state='disabled', command=self.plotWBHeatMap)
self.visMenu.add_command(label="Gene expression", state='disabled', command=self.plotGeneExpOntSNE)
self.config(menu=self.menubar)
#intro screen
tk.Label(self, text=u"Wishbone", font=('Helvetica', 48), fg="black", bg="white", padx=100, pady=50).grid(row=0)
tk.Label(self, text=u"To get started, select a data file by clicking File > Load Data", fg="black", bg="white", padx=100, pady=25).grid(row=1)
#update
self.protocol('WM_DELETE_WINDOW', self.quitWB)
self.grid_columnconfigure(0,weight=1)
self.resizable(True,True)
self.update()
self.geometry(self.geometry())
self.focus_force()
def loadData(self):
self.dataFileName = filedialog.askopenfilename(title='Load data file', initialdir='~/.wishbone/data')
if(self.dataFileName != ""):
#pop up data options menu
self.fileInfo = tk.Toplevel()
self.fileInfo.title("Data options")
tk.Label(self.fileInfo, text=u"File name: ").grid(column=0, row=0)
tk.Label(self.fileInfo, text=self.dataFileName.split('/')[-1]).grid(column=1, row=0)
tk.Label(self.fileInfo,text=u"Name:" ,fg="black",bg="white").grid(column=0, row=1)
self.fileNameEntryVar = tk.StringVar()
tk.Entry(self.fileInfo, textvariable=self.fileNameEntryVar).grid(column=1,row=1)
self.normalizeVar = tk.BooleanVar()
tk.Checkbutton(self.fileInfo, text=u"Normalize", variable=self.normalizeVar).grid(column=0, row=2, columnspan=2)
tk.Label(self.fileInfo, text=u"The normalize parameter is used for correcting for library size among cells.").grid(column=0, row=3, columnspan=2)
tk.Button(self.fileInfo, text="Cancel", command=self.fileInfo.destroy).grid(column=0, row=4)
tk.Button(self.fileInfo, text="Load", command=self.processData).grid(column=1, row=4)
self.wait_window(self.fileInfo)
def processData(self):
#clear intro screen
for item in self.grid_slaves():
item.grid_forget()
#load data
self.scdata = wishbone.wb.SCData.from_csv(os.path.expanduser(self.dataFileName),
data_type='sc-seq', normalize=self.normalizeVar.get())
#get genes
self.genes = self.scdata.data.columns.values
#display file name
tk.Label(self,text=u"File name: " + self.fileNameEntryVar.get(), fg="black",bg="white").grid(column=0,row=0)
#set up canvas for plots
self.fig, self.ax = wishbone.wb.get_fig()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='NSEW')
#set up visualization buttons
tk.Label(self, text=u"Visualizations:", fg='black', bg='white').grid(column=0, row=1)
self.PCAButton = tk.Button(self, text=u"PCA", state='disabled', command=self.plotPCA)
self.PCAButton.grid(column=0, row=2)
self.tSNEButton = tk.Button(self, text=u"tSNE", state='disabled', command=self.plotTSNE)
self.tSNEButton.grid(column=0, row=3)
self.DMButton = tk.Button(self, text=u"Diffusion map", state='disabled', command=self.plotDM)
self.DMButton.grid(column=0, row=4)
self.GSEAButton = tk.Button(self, text=u"GSEA Results", state='disabled', command=self.showGSEAResults)
self.GSEAButton.grid(column=0, row=5)
self.WBButton = tk.Button(self, text=u"Wishbone", state='disabled', command=self.plotWBOnTsne)
self.WBButton.grid(column=0, row=6)
self.geneExpButton = tk.Button(self, text=u"Gene expression", state='disabled', command=self.plotGeneExpOntSNE)
self.geneExpButton.grid(column=0, row=7)
self.saveButton = tk.Button(self, text=u"Save plot", state='disabled', command=self.savePlot)
self.saveButton.grid(column = 4, row=0)
self.diff_component = tk.StringVar()
self.diff_component.set('Component 1')
self.component_menu = tk.OptionMenu(self, self.diff_component,
'Component 1', 'Component 2', 'Component 3',
'Component 4', 'Component 5', 'Component 6',
'Component 7', 'Component 8', 'Component 9')
self.component_menu.config(state='disabled')
self.component_menu.grid(row=0, column=2)
self.updateButton = tk.Button(self, text=u"Update component", command=self.updateComponent, state='disabled')
self.updateButton.grid(column=3, row=0)
#enable buttons
self.analysisMenu.entryconfig(0, state='normal')
self.geometry('800x550')
#destroy pop up menu
self.fileInfo.destroy()
def runPCA(self):
self.scdata.run_pca()
#enable buttons
self.analysisMenu.entryconfig(1, state='normal')
self.visMenu.entryconfig(0, state='normal')
self.PCAButton.config(state='normal')
def runTSNE(self):
#pop up for # components
self.tsneOptions = tk.Toplevel()
self.tsneOptions.title("tSNE options")
tk.Label(self.tsneOptions,text=u"Number of components:" ,fg="black",bg="white").grid(column=0, row=0)
self.nCompVar = tk.IntVar()
self.nCompVar.set(5)
tk.Entry(self.tsneOptions, textvariable=self.nCompVar).grid(column=1,row=0)
tk.Button(self.tsneOptions, text="Run", command=self._runTSNE).grid(column=1, row=1)
tk.Button(self.tsneOptions, text="Cancel", command=self.tsneOptions.destroy).grid(column=0, row=1)
self.wait_window(self.tsneOptions)
def _runTSNE(self):
self.scdata.run_tsne(n_components=self.nCompVar.get())
#enable buttons
self.analysisMenu.entryconfig(2, state='normal')
self.visMenu.entryconfig(1, state='normal')
self.visMenu.entryconfig(5, state='normal')
self.tSNEButton.config(state='normal')
self.geneExpButton.config(state='normal')
self.tsneOptions.destroy()
def runDM(self):
self.scdata.run_diffusion_map()
#enable buttons
self.analysisMenu.entryconfig(3, state='normal')
self.analysisMenu.entryconfig(4, state='normal')
self.visMenu.entryconfig(2, state='normal')
self.DMButton.config(state='normal')
def runGSEA(self):
self.GSEAFileName = filedialog.askopenfilename(title='Select gmt File', initialdir='~/.wishbone/tools')
if self.GSEAFileName != "":
self.scdata.run_diffusion_map_correlations()
self.scdata.data.columns = self.scdata.data.columns.str.upper()
self.outputPrefix = filedialog.asksaveasfilename(title='Input file prefix for saving output', initialdir='~/.wishbone/gsea')
if 'mouse' in self.GSEAFileName:
gmt_file_type = 'mouse'
else:
gmt_file_type = 'human'
self.reports = self.scdata.run_gsea(output_stem= os.path.expanduser(self.outputPrefix),
gmt_file=(gmt_file_type, self.GSEAFileName.split('/')[-1]))
#enable buttons
self.visMenu.entryconfig(3, state='normal')
self.GSEAButton.config(state='normal')
def runWishbone(self):
#popup menu for wishbone options
self.wbOptions = tk.Toplevel()
self.wbOptions.title("Wishbone Options")
#s
tk.Label(self.wbOptions,text=u"Start cell:",fg="black",bg="white").grid(column=0,row=0)
self.start = tk.StringVar()
tk.Entry(self.wbOptions, textvariable=self.start).grid(column=1,row=0)
#k
tk.Label(self.wbOptions,text=u"k:",fg="black",bg="white").grid(column=0,row=1)
self.k = tk.IntVar()
tk.Entry(self.wbOptions, textvariable=self.k).grid(column=1,row=1)
self.k.set(15)
#components list
tk.Label(self.wbOptions, text=u"Components list:", fg='black', bg='white').grid(column=0, row=2)
self.compList = tk.StringVar()
tk.Entry(self.wbOptions, textvariable=self.compList).grid(column=1, row=2)
self.compList.set("1, 2, 3")
#num waypoints
tk.Label(self.wbOptions, text=u"Number of waypoints:", fg='black', bg='white').grid(column=0, row=3)
self.numWaypoints = tk.IntVar()
tk.Entry(self.wbOptions, textvariable=self.numWaypoints).grid(column=1, row=3)
self.numWaypoints.set(250)
#branch
self.branch = tk.BooleanVar()
self.branch.set(True)
tk.Checkbutton(self.wbOptions, text=u"Branch", variable=self.branch).grid(column=0, row=4, columnspan=2)
tk.Button(self.wbOptions, text="Run", command=self._runWishbone).grid(column=1, row=5)
tk.Button(self.wbOptions, text="Cancel", command=self.wbOptions.destroy).grid(column=0, row=5)
self.wait_window(self.wbOptions)
def _runWishbone(self):
self.wb = wishbone.wb.Wishbone(self.scdata)
self.wb.run_wishbone(start_cell=self.start.get(), k=self.k.get(), components_list=[int(comp) for comp in self.compList.get().split(',')], num_waypoints=self.numWaypoints.get())
#enable buttons
self.wishboneMenu.entryconfig(0, state='normal')
self.wishboneMenu.entryconfig(1, state='normal')
self.wishboneMenu.entryconfig(2, state='normal')
self.WBButton.config(state='normal')
self.wbOptions.destroy()
def plotPCA(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
#pop up for # components
self.PCAOptions = tk.Toplevel()
self.PCAOptions.title("PCA Plot Options")
tk.Label(self.PCAOptions,text=u"Max variance explained (ylim):",fg="black",bg="white").grid(column=0, row=0)
self.yLimVar = tk.DoubleVar()
self.yLimVar.set(round(self.scdata.pca['eigenvalues'][0][0], 2))
tk.Entry(self.PCAOptions, textvariable=self.yLimVar).grid(column=1,row=0)
tk.Label(self.PCAOptions, text=u"Number of components:", fg='black', bg='white').grid(column=0, row=1)
self.compVar = tk.IntVar()
self.compVar.set(15)
tk.Entry(self.PCAOptions, textvariable=self.compVar).grid(column=1, row=1)
tk.Button(self.PCAOptions, text="Plot", command=self._plotPCA).grid(column=1, row=2)
tk.Button(self.PCAOptions, text="Cancel", command=self.PCAOptions.destroy).grid(column=0, row=2)
self.wait_window(self.PCAOptions)
def _plotPCA(self):
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_pca_variance_explained(ylim=(0, self.yLimVar.get()), n_components=self.compVar.get())
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='NW')
self.currentPlot = 'pca'
#enable buttons
self.saveButton.config(state='normal')
self.PCAOptions.destroy()
def plotTSNE(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_tsne()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='NW')
self.currentPlot = 'tsne'
def plotDM(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.geometry('950x550')
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_diffusion_components()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='W')
self.currentPlot = 'dm_components'
def showGSEAResults(self):
self.saveButton.config(state='disabled')
self.component_menu.config(state='normal')
self.updateButton.config(state='normal')
self.resetCanvas()
self.canvas = tk.Canvas(self, width=600, height=300)
self.canvas.grid(column=1, row=1, rowspan=17, columnspan=4)
self.outputText(1)
self.currentPlot = 'GSEA_result_'+self.diff_component.get()
def updateComponent(self):
self.resetCanvas()
self.canvas = tk.Canvas(self, width=600, height=300)
self.canvas.grid(column=1, row=1, rowspan=17, columnspan=4,sticky='NSEW')
self.outputText(int(self.diff_component.get().split(' ')[-1]))
self.currentPlot = 'GSEA_result_'+self.diff_component.get()
def outputText(self, diff_component):
pos_text = str(self.reports[diff_component]['pos']).split('\n')
pos_text = pos_text[1:len(pos_text)-1]
pos_text = '\n'.join(pos_text)
neg_text = str(self.reports[diff_component]['neg']).split('\n')
neg_text = neg_text[1:len(neg_text)-1]
neg_text = '\n'.join(neg_text)
self.canvas.create_text(5, 5, anchor='nw', text='Positive correlations:\n\n', font=('Helvetica', 16, 'bold'))
self.canvas.create_text(5, 50, anchor='nw', text=pos_text)
self.canvas.create_text(5, 150, anchor='nw', text='Negative correlations:\n\n', font=('Helvetica', 16, 'bold'))
self.canvas.create_text(5, 200, anchor='nw', text=neg_text)
def plotWBOnTsne(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.resetCanvas()
self.fig, self.ax = self.wb.plot_wishbone_on_tsne()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4)
self.currentPlot = 'wishbone_on_tsne'
def plotWBMarkerTrajectory(self):
self.getGeneSelection()
if len(self.selectedGenes) < 1:
print('Error: must select at least one gene')
else:
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.resetCanvas()
self.vals, self.fig, self.ax = self.wb.plot_marker_trajectory(self.selectedGenes)
self.fig.set_size_inches(10, 4, forward=True)
self.fig.tight_layout()
self.fig.subplots_adjust(right=0.8)
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=5, sticky='W')
self.currentPlot = 'wishbone_marker_trajectory'
self.geometry('1050x550')
#enable buttons
self.wishboneMenu.entryconfig(2, state='normal')
def plotWBHeatMap(self):
self.getGeneSelection()
if len(self.selectedGenes) < 1:
print('Error: must select at least one gene')
else:
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.resetCanvas()
self.vals, self.fig, self.ax = self.wb.plot_marker_trajectory(self.selectedGenes)
self.fig, self.ax = self.wb.plot_marker_heatmap(self.vals)
self.fig.set_size_inches(10, 4, forward=True)
self.fig.tight_layout()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=5, sticky='W')
self.currentPlot = 'wishbone_marker_heatmap'
def plotGeneExpOntSNE(self):
self.getGeneSelection()
if len(self.selectedGenes) < 1:
print('Error: must select at least one gene')
else:
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_gene_expression(self.selectedGenes)
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.show()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4,sticky='W')
self.currentPlot = 'gene_expression_tsne'
self.geometry('950x550')
def getGeneSelection(self):
#popup menu to get selected genes
self.geneSelection = tk.Toplevel()
self.geneSelection.title("Select Genes")
tk.Label(self.geneSelection,text=u"Genes:",fg="black",bg="white").grid(row=0)
self.geneInput = wishbone.autocomplete_entry.AutocompleteEntry(self.genes.tolist(), self.geneSelection, listboxLength=6)
self.geneInput.grid(row=1)
self.geneInput.bind('<Return>', self.AddToSelected)
self.geneSelectBox = tk.Listbox(self.geneSelection, selectmode=tk.EXTENDED)
self.geneSelectBox.grid(row=2, rowspan=10)
self.geneSelectBox.bind('<BackSpace>', self.DeleteSelected)
self.selectedGenes = []
tk.Button(self.geneSelection, text="Use selected genes", command=self.geneSelection.destroy).grid(row=12)
tk.Button(self.geneSelection, text="Cancel", command=self.cancelGeneSelection).grid(row=13)
self.wait_window(self.geneSelection)
def cancelGeneSelection(self):
self.selectedGenes = []
self.geneSelection.destroy()
def AddToSelected(self, event):
self.selectedGenes.append(self.geneInput.get())
self.geneSelectBox.insert(tk.END, self.selectedGenes[len(self.selectedGenes)-1])
def DeleteSelected(self, event):
selected = self.geneSelectBox.curselection()
pos = 0
for i in selected:
idx = int(i) - pos
self.geneSelectBox.delete( idx,idx )
self.selectedGenes = self.selectedGenes[:idx] + self.selectedGenes[idx+1:]
pos = pos + 1
def savePlot(self):
self.plotFileName = filedialog.asksaveasfilename(title='Save Plot', defaultextension='.png', initialfile=self.fileNameEntryVar.get()+"_"+self.currentPlot)
if self.plotFileName != None:
self.fig.savefig(self.plotFileName)
def resetCanvas(self):
self.fig.clf()
if type(self.canvas) is FigureCanvasTkAgg:
for item in self.canvas.get_tk_widget().find_all():
self.canvas.get_tk_widget().delete(item)
else:
for item in self.canvas.find_all():
self.canvas.delete(item)
def quitWB(self):
self.quit()
self.destroy()
class wishbone_gui(tk.Tk):
def __init__(self, parent):
tk.Tk.__init__(self, parent)
self.parent = parent
self.initialize()
def initialize(self):
self.grid()
self.vals = None
self.currentPlot = None
# set up menu bar
self.menubar = tk.Menu(self)
self.fileMenu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="File", menu=self.fileMenu)
self.fileMenu.add_command(label="Load data", command=self.loadData)
self.fileMenu.add_command(
label="Save data", state="disabled", command=self.saveData
)
self.fileMenu.add_command(label="Exit Wishbone", command=self.quitWB)
self.analysisMenu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="Analysis", menu=self.analysisMenu)
self.analysisMenu.add_command(
label="Principal component analysis", state="disabled", command=self.runPCA
)
self.analysisMenu.add_command(
label="tSNE", state="disabled", command=self.runTSNE
)
self.analysisMenu.add_command(
label="Diffusion map", state="disabled", command=self.runDM
)
self.analysisMenu.add_command(
label="GSEA", state="disabled", command=self.runGSEA
)
self.analysisMenu.add_command(
label="Wishbone", state="disabled", command=self.runWishbone
)
self.visMenu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="Visualization", menu=self.visMenu)
self.visMenu.add_command(
label="Principal component analysis", state="disabled", command=self.plotPCA
)
self.visMenu.add_command(label="tSNE", state="disabled", command=self.plotTSNE)
self.visMenu.add_command(
label="Diffusion map", state="disabled", command=self.plotDM
)
self.visMenu.add_command(
label="GSEA Results", state="disabled", command=self.showGSEAResults
)
self.wishboneMenu = tk.Menu(self)
self.visMenu.add_cascade(label="Wishbone", menu=self.wishboneMenu)
self.wishboneMenu.add_command(
label="On tSNE", state="disabled", command=self.plotWBOnTsne
)
self.wishboneMenu.add_command(
label="Marker trajectory",
state="disabled",
command=self.plotWBMarkerTrajectory,
)
self.wishboneMenu.add_command(
label="Heat map", state="disabled", command=self.plotWBHeatMap
)
self.visMenu.add_command(
label="Gene expression", state="disabled", command=self.plotGeneExpOntSNE
)
self.visMenu.add_command(
label="Set gate", state="disabled", command=self.setGate
)
self.config(menu=self.menubar)
# intro screen
tk.Label(
self,
text=u"Wishbone",
font=("Helvetica", 48),
fg="black",
bg="white",
padx=100,
pady=50,
).grid(row=0)
tk.Label(
self,
text=u"To get started, select a data file by clicking File > Load Data",
fg="black",
bg="white",
padx=100,
pady=25,
).grid(row=1)
# update
self.protocol("WM_DELETE_WINDOW", self.quitWB)
self.grid_columnconfigure(0, weight=1)
self.resizable(True, True)
self.update()
self.geometry(self.geometry())
self.focus_force()
def loadData(self):
self.dataFileName = filedialog.askopenfilename(
title="Load data file", initialdir="~/.wishbone/data"
)
if self.dataFileName != "":
# pop up data options menu
self.fileInfo = tk.Toplevel()
self.fileInfo.title("Data options")
tk.Label(self.fileInfo, text=u"File name: ").grid(column=0, row=0)
tk.Label(self.fileInfo, text=self.dataFileName.split("/")[-1]).grid(
column=1, row=0
)
tk.Label(self.fileInfo, text=u"Name:", fg="black", bg="white").grid(
column=0, row=1
)
self.fileNameEntryVar = tk.StringVar()
tk.Entry(self.fileInfo, textvariable=self.fileNameEntryVar).grid(
column=1, row=1
)
if (
self.dataFileName.split(".")[len(self.dataFileName.split(".")) - 1]
== "fcs"
):
tk.Label(self.fileInfo, text=u"Cofactor:", fg="black", bg="white").grid(
column=0, row=2
)
self.cofactorVar = tk.IntVar()
self.cofactorVar.set(5)
tk.Entry(self.fileInfo, textvariable=self.cofactorVar).grid(
column=1, row=2
)
elif (
self.dataFileName.split(".")[len(self.dataFileName.split(".")) - 1]
== "csv"
):
self.normalizeVar = tk.BooleanVar()
tk.Checkbutton(
self.fileInfo, text=u"Normalize", variable=self.normalizeVar
).grid(column=0, row=2, columnspan=2)
tk.Label(
self.fileInfo,
text=u"The normalize parameter is used for correcting for library "
u"size among cells.",
).grid(column=0, row=3, columnspan=2)
tk.Button(self.fileInfo, text="Cancel", command=self.fileInfo.destroy).grid(
column=0, row=4
)
tk.Button(self.fileInfo, text="Load", command=self.processData).grid(
column=1, row=4
)
self.wait_window(self.fileInfo)
def processData(self):
# clear intro screen
for item in self.grid_slaves():
item.grid_forget()
# display file name
tk.Label(
self,
text=u"File name: " + self.fileNameEntryVar.get(),
fg="black",
bg="white",
).grid(column=0, row=0)
# set up canvas for plots
self.fig, self.ax = wishbone.wb.get_fig()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.draw()
self.canvas.get_tk_widget().grid(
column=1, row=1, rowspan=10, columnspan=4, sticky="NSEW"
)
tk.Label(self, text=u"Visualizations:", fg="black", bg="white").grid(
column=0, row=1
)
# load data based on input type
if (
self.dataFileName.split(".")[
len(self.dataFileName.split(".")) - 1] == "fcs"
): # mass cytometry data
self.scdata = wishbone.wb.SCData.from_fcs(
os.path.expanduser(self.dataFileName), cofactor=self.cofactorVar.get()
)
self.wb = None
elif (
self.dataFileName.split(".")[
len(self.dataFileName.split(".")) - 1] == "csv"
): # sc-seq data
self.scdata = wishbone.wb.SCData.from_csv(
os.path.expanduser(self.dataFileName),
data_type="sc-seq",
normalize=self.normalizeVar.get(),
)
self.wb = None
else:
self.wb = wishbone.wb.Wishbone.load(self.dataFileName)
self.scdata = self.wb.scdata
# set up buttons based on data type
if self.scdata.data_type == "sc-seq":
self.PCAButton = tk.Button(
self, text=u"PCA", state="disabled", command=self.plotPCA
)
self.PCAButton.grid(column=0, row=2)
self.tSNEButton = tk.Button(
self, text=u"tSNE", state="disabled", command=self.plotTSNE
)
self.tSNEButton.grid(column=0, row=3)
self.DMButton = tk.Button(
self, text=u"Diffusion map", state="disabled", command=self.plotDM
)
self.DMButton.grid(column=0, row=4)
self.GSEAButton = tk.Button(
self,
text=u"GSEA Results",
state="disabled",
command=self.showGSEAResults,
)
self.GSEAButton.grid(column=0, row=5)
self.WBButton = tk.Button(
self, text=u"Wishbone", state="disabled", command=self.plotWBOnTsne
)
self.WBButton.grid(column=0, row=6)
self.geneExpButton = tk.Button(
self,
text=u"Gene expression",
state="disabled",
command=self.plotGeneExpOntSNE,
)
self.geneExpButton.grid(column=0, row=7)
self.setGateButton = tk.Button(
self, text=u"Set gate", state="disabled", command=self.setGate
)
self.setGateButton.grid(column=0, row=8)
self.saveButton = tk.Button(
self, text=u"Save plot", state="disabled", command=self.savePlot
)
self.saveButton.grid(column=4, row=0)
self.diff_component = tk.StringVar()
self.diff_component.set("Component 1")
self.component_menu = tk.OptionMenu(
self,
self.diff_component,
"Component 1",
"Component 2",
"Component 3",
"Component 4",
"Component 5",
"Component 6",
"Component 7",
"Component 8",
"Component 9",
)
self.component_menu.config(state="disabled")
self.component_menu.grid(row=0, column=2)
self.updateButton = tk.Button(
self,
text=u"Update component",
command=self.updateComponent,
state="disabled",
)
self.updateButton.grid(column=3, row=0)
# enable buttons based on current state of scdata object
if self.scdata.pca:
self.analysisMenu.entryconfig(1, state="normal")
self.visMenu.entryconfig(0, state="normal")
self.PCAButton.config(state="normal")
if isinstance(self.scdata.tsne, pd.DataFrame):
self.analysisMenu.entryconfig(2, state="normal")
self.visMenu.entryconfig(1, state="normal")
self.visMenu.entryconfig(5, state="normal")
self.tSNEButton.config(state="normal")
self.geneExpButton.config(state="normal")
if isinstance(self.scdata.diffusion_eigenvectors, pd.DataFrame):
self.analysisMenu.entryconfig(3, state="normal")
self.analysisMenu.entryconfig(4, state="normal")
self.visMenu.entryconfig(2, state="normal")
self.DMButton.config(state="normal")
else:
self.tSNEButton = tk.Button(
self, text=u"tSNE", state="disabled", command=self.plotTSNE
)
self.tSNEButton.grid(column=0, row=2)
self.DMButton = tk.Button(
self, text=u"Diffusion map", state="disabled", command=self.plotDM
)
self.DMButton.grid(column=0, row=3)
self.WBButton = tk.Button(
self, text=u"Wishbone", state="disabled", command=self.plotWBOnTsne
)
self.WBButton.grid(column=0, row=4)
self.geneExpButton = tk.Button(
self,
text=u"Gene expression",
state="disabled",
command=self.plotGeneExpOntSNE,
)
self.geneExpButton.grid(column=0, row=5)
self.setGateButton = tk.Button(
self, text=u"Set gate", state="disabled", command=self.setGate
)
self.setGateButton.grid(column=0, row=6)
self.saveButton = tk.Button(
self, text=u"Save plot", state="disabled", command=self.savePlot
)
self.saveButton.grid(column=4, row=0)
self.analysisMenu.delete(0)
self.analysisMenu.delete(2)
self.visMenu.delete(0)
self.visMenu.delete(2)
self.analysisMenu.entryconfig(1, state="normal")
# enable buttons based on current state of scdata object
if isinstance(self.scdata.tsne, pd.DataFrame):
self.visMenu.entryconfig(0, state="normal")
self.visMenu.entryconfig(3, state="normal")
self.tSNEButton.config(state="normal")
self.geneExpButton.config(state="normal")
if isinstance(self.scdata.diffusion_eigenvectors, pd.DataFrame):
self.analysisMenu.entryconfig(2, state="normal")
self.visMenu.entryconfig(1, state="normal")
self.DMButton.config(state="normal")
# enable buttons
self.analysisMenu.entryconfig(0, state="normal")
self.fileMenu.entryconfig(1, state="normal")
if self.wb:
if isinstance(self.wb.trajectory, pd.Series):
self.wishboneMenu.entryconfig(0, state="normal")
self.wishboneMenu.entryconfig(1, state="normal")
self.wishboneMenu.entryconfig(2, state="normal")
self.WBButton.config(state="normal")
# get genes
self.genes = self.scdata.data.columns.values
self.gates = {}
self.geometry("800x550")
# destroy pop up menu
self.fileInfo.destroy()
def saveData(self):
pickleFileName = filedialog.asksaveasfilename(
title="Save Wishbone Data",
defaultextension=".p",
initialfile=self.fileNameEntryVar.get(),
)
if pickleFileName != None:
if self.wb != None:
self.wb.save(pickleFileName)
else:
self.scdata.save_as_wishbone(pickleFileName)
def runPCA(self):
self.scdata.run_pca()
# enable buttons
self.analysisMenu.entryconfig(1, state="normal")
self.visMenu.entryconfig(0, state="normal")
self.PCAButton.config(state="normal")
def runTSNE(self):
# pop up for # components
self.tsneOptions = tk.Toplevel()
self.tsneOptions.title("tSNE options")
if self.scdata.data_type == "sc-seq":
tk.Label(
self.tsneOptions, text=u"Number of components:", fg="black", bg="white"
).grid(column=0, row=0)
self.nCompVar = tk.IntVar()
self.nCompVar.set(15)
tk.Entry(self.tsneOptions, textvariable=self.nCompVar).grid(column=1, row=0)
tk.Label(self.tsneOptions, text=u"Perplexity:", fg="black", bg="white").grid(
column=0, row=1
)
self.perplexityVar = tk.IntVar()
self.perplexityVar.set(30)
tk.Entry(self.tsneOptions, textvariable=self.perplexityVar).grid(
column=1, row=1
)
tk.Button(self.tsneOptions, text="Run", command=self._runTSNE).grid(
column=1, row=2
)
tk.Button(
self.tsneOptions, text="Cancel", command=self.tsneOptions.destroy
).grid(column=0, row=2)
self.wait_window(self.tsneOptions)
def _runTSNE(self):
if self.scdata.data_type == "sc-seq":
self.scdata.run_tsne(
n_components=self.nCompVar.get(), perplexity=self.perplexityVar.get()
)
else:
self.scdata.run_tsne(n_components=None, perplexity=self.perplexityVar.get())
self.gates = {}
# enable buttons
if self.scdata.data_type == "sc-seq":
self.analysisMenu.entryconfig(2, state="normal")
self.visMenu.entryconfig(1, state="normal")
self.visMenu.entryconfig(5, state="normal")
else:
self.visMenu.entryconfig(0, state="normal")
self.visMenu.entryconfig(3, state="normal")
self.tSNEButton.config(state="normal")
self.geneExpButton.config(state="normal")
self.tsneOptions.destroy()
def runDM(self):
self.scdata.run_diffusion_map()
# enable buttons
if self.scdata.data_type == "sc-seq":
self.analysisMenu.entryconfig(3, state="normal")
self.analysisMenu.entryconfig(4, state="normal")
self.visMenu.entryconfig(2, state="normal")
else:
self.analysisMenu.entryconfig(2, state="normal")
self.visMenu.entryconfig(1, state="normal")
self.DMButton.config(state="normal")
def runGSEA(self):
self.GSEAFileName = filedialog.askopenfilename(
title="Select gmt File", initialdir="~/.wishbone/tools"
)
if self.GSEAFileName != "":
self.scdata.run_diffusion_map_correlations()
self.scdata.data.columns = self.scdata.data.columns.str.upper()
self.outputPrefix = filedialog.asksaveasfilename(
title="Input file prefix for saving output",
initialdir="~/.wishbone/gsea",
)
if "mouse" in self.GSEAFileName:
gmt_file_type = "mouse"
else:
gmt_file_type = "human"
self.reports = self.scdata.run_gsea(
output_stem=os.path.expanduser(self.outputPrefix),
gmt_file=(gmt_file_type, self.GSEAFileName.split("/")[-1]),
)
# enable buttons
self.visMenu.entryconfig(3, state="normal")
self.GSEAButton.config(state="normal")
def runWishbone(self):
# popup menu for wishbone options
self.wbOptions = tk.Toplevel()
self.wbOptions.title("Wishbone Options")
# s
tk.Label(self.wbOptions, text=u"Start cell:", fg="black", bg="white").grid(
column=0, row=0
)
self.start = tk.StringVar()
tk.Entry(self.wbOptions, textvariable=self.start).grid(column=1, row=0)
if len(self.gates) > 0:
self.cell_gate = tk.StringVar()
self.cell_gate.set("Use cell gate")
self.gate_menu = tk.OptionMenu(
self.wbOptions, self.cell_gate, *list(self.gates.keys())
)
self.gate_menu.grid(row=0, column=2)
# k
tk.Label(self.wbOptions, text=u"k:", fg="black", bg="white").grid(
column=0, row=1
)
self.k = tk.IntVar()
tk.Entry(self.wbOptions, textvariable=self.k).grid(column=1, row=1)
self.k.set(15)
# components list
tk.Label(self.wbOptions, text=u"Components list:", fg="black", bg="white").grid(
column=0, row=2
)
self.compList = tk.StringVar()
tk.Entry(self.wbOptions, textvariable=self.compList).grid(column=1, row=2)
self.compList.set("1, 2, 3")
# num waypoints
tk.Label(
self.wbOptions, text=u"Number of waypoints:", fg="black", bg="white"
).grid(column=0, row=3)
self.numWaypoints = tk.IntVar()
tk.Entry(self.wbOptions, textvariable=self.numWaypoints).grid(column=1, row=3)
self.numWaypoints.set(250)
# branch
self.branch = tk.BooleanVar()
self.branch.set(True)
tk.Checkbutton(self.wbOptions, text=u"Branch", variable=self.branch).grid(
column=0, row=4, columnspan=2
)
tk.Button(self.wbOptions, text="Run", command=self._runWishbone).grid(
column=1, row=5
)
tk.Button(self.wbOptions, text="Cancel", command=self.wbOptions.destroy).grid(
column=0, row=5
)
self.wait_window(self.wbOptions)
def _runWishbone(self):
self.wb = wishbone.wb.Wishbone(self.scdata)
if self.cell_gate.get() == "Use cell gate":
self.wb.run_wishbone(
start_cell=self.start.get(),
k=self.k.get(),
components_list=[int(comp) for comp in self.compList.get().split(",")],
num_waypoints=self.numWaypoints.get(),
branch=self.branch.get(),
)
else:
# randomly select start cell in gate
print("Using cell gate:")
print(self.cell_gate.get())
start_cell = random.sample(list(self.gates[self.cell_gate.get()]), 1)[0]
print(start_cell)
self.wb.run_wishbone(
start_cell=start_cell,
k=self.k.get(),
components_list=[int(comp) for comp in self.compList.get().split(",")],
num_waypoints=self.numWaypoints.get(),
branch=self.branch.get(),
)
# enable buttons
self.wishboneMenu.entryconfig(0, state="normal")
self.wishboneMenu.entryconfig(1, state="normal")
self.wishboneMenu.entryconfig(2, state="normal")
self.WBButton.config(state="normal")
self.wbOptions.destroy()
def plotPCA(self):
self.saveButton.config(state="normal")
self.setGateButton.config(state="disabled")
if self.scdata.data_type == "sc-seq":
self.component_menu.config(state="disabled")
self.updateButton.config(state="disabled")
self.visMenu.entryconfig(6, state="disabled")
else:
self.visMenu.entryconfig(4, state="disabled")
# pop up for # components
self.PCAOptions = tk.Toplevel()
self.PCAOptions.title("PCA Plot Options")
tk.Label(
self.PCAOptions,
text=u"Max variance explained (ylim):",
fg="black",
bg="white",
).grid(column=0, row=0)
self.yLimVar = tk.DoubleVar()
self.yLimVar.set(round(self.scdata.pca["eigenvalues"][0][0], 2))
tk.Entry(self.PCAOptions, textvariable=self.yLimVar).grid(column=1, row=0)
tk.Label(
self.PCAOptions, text=u"Number of components:", fg="black", bg="white"
).grid(column=0, row=1)
self.compVar = tk.IntVar()
self.compVar.set(15)
tk.Entry(self.PCAOptions, textvariable=self.compVar).grid(column=1, row=1)
tk.Button(self.PCAOptions, text="Plot", command=self._plotPCA).grid(
column=1, row=2
)
tk.Button(self.PCAOptions, text="Cancel", command=self.PCAOptions.destroy).grid(
column=0, row=2
)
self.wait_window(self.PCAOptions)
def _plotPCA(self):
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_pca_variance_explained(
ylim=(0, self.yLimVar.get()), n_components=self.compVar.get()
)
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.draw()
self.canvas.get_tk_widget().grid(
column=1, row=1, rowspan=10, columnspan=4, sticky="NW"
)
self.currentPlot = "pca"
# enable buttons
self.saveButton.config(state="normal")
self.PCAOptions.destroy()
def plotTSNE(self):
self.saveButton.config(state="normal")
self.setGateButton.config(state="normal")
if self.scdata.data_type == "sc-seq":
self.component_menu.config(state="disabled")
self.updateButton.config(state="disabled")
self.visMenu.entryconfig(6, state="normal")
else:
self.visMenu.entryconfig(4, state="normal")
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_tsne()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.draw()
self.canvas.get_tk_widget().grid(
column=1, row=1, rowspan=10, columnspan=4, sticky="NW"
)
self.currentPlot = "tsne"
def plotDM(self):
self.saveButton.config(state="normal")
self.setGateButton.config(state="disabled")
if self.scdata.data_type == "sc-seq":
self.component_menu.config(state="disabled")
self.updateButton.config(state="disabled")
self.visMenu.entryconfig(6, state="disabled")
else:
self.visMenu.entryconfig(4, state="disabled")
self.geometry("950x550")
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_diffusion_components()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.draw()
self.canvas.get_tk_widget().grid(
column=1, row=1, rowspan=10, columnspan=4, sticky="W"
)
self.currentPlot = "dm_components"
def showGSEAResults(self):
self.saveButton.config(state="disabled")
self.component_menu.config(state="normal")
self.updateButton.config(state="normal")
self.setGateButton.config(state="disabled")
self.visMenu.entryconfig(6, state="disabled")
self.resetCanvas()
self.canvas = tk.Canvas(self, width=600, height=300)
self.canvas.grid(column=1, row=1, rowspan=17, columnspan=4)
self.outputText(1)
self.currentPlot = "GSEA_result_" + self.diff_component.get()
def updateComponent(self):
self.resetCanvas()
self.canvas = tk.Canvas(self, width=600, height=300)
self.canvas.grid(column=1, row=1, rowspan=17, columnspan=4, sticky="NSEW")
self.outputText(int(self.diff_component.get().split(" ")[-1]))
self.currentPlot = "GSEA_result_" + self.diff_component.get()
def outputText(self, diff_component):
pos_text = str(self.reports[diff_component]["pos"]).split("\n")
pos_text = pos_text[1: len(pos_text) - 1]
pos_text = "\n".join(pos_text)
neg_text = str(self.reports[diff_component]["neg"]).split("\n")
neg_text = neg_text[1: len(neg_text) - 1]
neg_text = "\n".join(neg_text)
self.canvas.create_text(
5,
5,
anchor="nw",
text="Positive correlations:\n\n",
font=("Helvetica", 16, "bold"),
)
self.canvas.create_text(5, 50, anchor="nw", text=pos_text)
self.canvas.create_text(
5,
150,
anchor="nw",
text="Negative correlations:\n\n",
font=("Helvetica", 16, "bold"),
)
self.canvas.create_text(5, 200, anchor="nw", text=neg_text)
def plotWBOnTsne(self):
self.saveButton.config(state="normal")
self.setGateButton.config(state="disabled")
if self.scdata.data_type == "sc-seq":
self.component_menu.config(state="disabled")
self.updateButton.config(state="disabled")
self.visMenu.entryconfig(6, state="disabled")
else:
self.visMenu.entryconfig(4, state="disabled")
self.resetCanvas()
self.fig, self.ax = self.wb.plot_wishbone_on_tsne()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.draw()
self.canvas.get_tk_widget().grid(column=1, row=1, rowspan=10, columnspan=4)
self.currentPlot = "wishbone_on_tsne"
def plotWBMarkerTrajectory(self):
self.getGeneSelection()
if len(self.selectedGenes) < 1:
print("Error: must select at least one gene")
else:
self.saveButton.config(state="normal")
self.setGateButton.config(state="disabled")
if self.scdata.data_type == "sc-seq":
self.component_menu.config(state="disabled")
self.updateButton.config(state="disabled")
self.visMenu.entryconfig(6, state="disabled")
else:
self.visMenu.entryconfig(4, state="disabled")
self.resetCanvas()
self.vals, self.fig, self.ax = self.wb.plot_marker_trajectory(
self.selectedGenes
)
self.fig.set_size_inches(10, 4, forward=True)
self.fig.tight_layout()
self.fig.subplots_adjust(right=0.8)
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.draw()
self.canvas.get_tk_widget().grid(
column=1, row=1, rowspan=10, columnspan=5, sticky="W"
)
self.currentPlot = "wishbone_marker_trajectory"
self.geometry("1050x550")
# enable buttons
self.wishboneMenu.entryconfig(2, state="normal")
def plotWBHeatMap(self):
self.getGeneSelection()
if len(self.selectedGenes) < 1:
print("Error: must select at least one gene")
else:
self.saveButton.config(state="normal")
self.setGateButton.config(state="disabled")
if self.scdata.data_type == "sc-seq":
self.component_menu.config(state="disabled")
self.updateButton.config(state="disabled")
self.visMenu.entryconfig(6, state="disabled")
else:
self.visMenu.entryconfig(4, state="disabled")
self.resetCanvas()
self.vals, self.fig, self.ax = self.wb.plot_marker_trajectory(
self.selectedGenes
)
self.fig, self.ax = self.wb.plot_marker_heatmap(self.vals)
self.fig.set_size_inches(10, 4, forward=True)
self.fig.tight_layout()
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.draw()
self.canvas.get_tk_widget().grid(
column=1, row=1, rowspan=10, columnspan=5, sticky="W"
)
self.currentPlot = "wishbone_marker_heatmap"
def plotGeneExpOntSNE(self):
self.getGeneSelection()
if len(self.selectedGenes) < 1:
print("Error: must select at least one gene")
else:
self.saveButton.config(state="normal")
self.setGateButton.config(state="disabled")
if self.scdata.data_type == "sc-seq":
self.component_menu.config(state="disabled")
self.updateButton.config(state="disabled")
self.visMenu.entryconfig(6, state="disabled")
else:
self.visMenu.entryconfig(4, state="disabled")
self.resetCanvas()
self.fig, self.ax = self.scdata.plot_gene_expression(self.selectedGenes)
self.canvas = FigureCanvasTkAgg(self.fig, self)
self.canvas.draw()
self.canvas.get_tk_widget().grid(
column=1, row=1, rowspan=10, columnspan=4, sticky="W"
)
self.currentPlot = "gene_expression_tsne"
self.geometry("950x550")
def getGeneSelection(self):
# popup menu to get selected genes
self.geneSelection = tk.Toplevel()
self.geneSelection.title("Select Genes")
tk.Label(self.geneSelection, text=u"Genes:", fg="black", bg="white").grid(row=0)
self.geneInput = wishbone.autocomplete_entry.AutocompleteEntry(
self.genes.tolist(), self.geneSelection, listboxLength=6
)
self.geneInput.grid(row=1)
self.geneInput.bind("<Return>", self.AddToSelected)
self.geneSelectBox = tk.Listbox(self.geneSelection, selectmode=tk.EXTENDED)
self.geneSelectBox.grid(row=2, rowspan=10)
self.geneSelectBox.bind("<BackSpace>", self.DeleteSelected)
self.selectedGenes = []
tk.Button(
self.geneSelection,
text="Use selected genes",
command=self.geneSelection.destroy,
).grid(row=12)
tk.Button(
self.geneSelection, text="Cancel", command=self.cancelGeneSelection
).grid(row=13)
self.wait_window(self.geneSelection)
def cancelGeneSelection(self):
self.selectedGenes = []
self.geneSelection.destroy()
def AddToSelected(self, event):
self.selectedGenes.append(self.geneInput.get())
self.geneSelectBox.insert(
tk.END, self.selectedGenes[len(self.selectedGenes) - 1]
)
def DeleteSelected(self, event):
selected = self.geneSelectBox.curselection()
pos = 0
for i in selected:
idx = int(i) - pos
self.geneSelectBox.delete(idx, idx)
self.selectedGenes = (
self.selectedGenes[:idx] + self.selectedGenes[idx + 1:]
)
pos = pos + 1
def savePlot(self):
self.plotFileName = filedialog.asksaveasfilename(
title="Save Plot",
defaultextension=".png",
initialfile=self.fileNameEntryVar.get() + "_" + self.currentPlot,
)
if self.plotFileName != None:
self.fig.savefig(self.plotFileName)
def setGate(self):
# pop up for gate name
self.gateOptions = tk.Toplevel()
self.gateOptions.title("Create gate for start cells")
tk.Label(self.gateOptions, text=u"Gate name:", fg="black", bg="white").grid(
column=0, row=0
)
self.gateName = tk.StringVar()
self.gateName.set("Gate " + str(len(self.gates) + 1))
tk.Entry(self.gateOptions, textvariable=self.gateName).grid(column=1, row=0)
tk.Button(self.gateOptions, text="Select gate", command=self._setGate).grid(
column=1, row=1
)
tk.Button(
self.gateOptions, text="Cancel", command=self.gateOptions.destroy
).grid(column=0, row=1)
self.wait_window(self.gateOptions)
def _setGate(self):
self.gateOptions.destroy()
self.buttonPress = self.canvas.mpl_connect(
"button_press_event", self._startGate
)
self.buttonRelease = self.canvas.mpl_connect(
"button_release_event", self._endGate
)
self.canvas.get_tk_widget().config(cursor="plus")
def _startGate(self, event):
self.start_x = event.xdata
self.start_y = event.ydata
def _endGate(self, event):
# draw gate rectangle
start_x = self.start_x if self.start_x < event.xdata else event.xdata
start_y = self.start_y if self.start_y < event.ydata else event.ydata
width = np.absolute(event.xdata - self.start_x)
height = np.absolute(event.ydata - self.start_y)
rect = Rectangle(
(start_x, start_y), width, height, fill=False, ec="black", alpha=1, lw=2
)
self.ax.add_patch(rect)
self.canvas.draw()
# disable mouse events
self.canvas.mpl_disconnect(self.buttonPress)
self.canvas.mpl_disconnect(self.buttonRelease)
self.canvas.get_tk_widget().config(cursor="arrow")
# save cell gate
gate = Path(
[
[start_x, start_y],
[start_x + width, start_y],
[start_x + width, start_y + height],
[start_x, start_y + height],
[start_x, start_y],
]
)
gated_cells = self.scdata.tsne.index[gate.contains_points(self.scdata.tsne)]
self.gates[self.gateName.get()] = gated_cells
# replot tSNE w gate colored
self.fig.clf()
plt.scatter(
self.scdata.tsne["x"],
self.scdata.tsne["y"],
s=10,
edgecolors="none",
color="lightgrey",
)
plt.scatter(
self.scdata.tsne.ix[gated_cells, "x"],
self.scdata.tsne.ix[gated_cells, "y"],
s=10,
edgecolors="none",
)
self.canvas.draw()
self.setGateButton.config(state="disabled")
self.visMenu.entryconfig(6, state="disabled")
def resetCanvas(self):
self.fig.clf()
if type(self.canvas) is FigureCanvasTkAgg:
for item in self.canvas.get_tk_widget().find_all():
self.canvas.get_tk_widget().delete(item)
else:
for item in self.canvas.find_all():
self.canvas.delete(item)
def quitWB(self):
self.quit()
self.destroy()
