def plot_line_graph(data_length):
lists = sorted(data_length.items())
line_graphs = []
protocols, data_lengths = zip(*lists)
i = 0
while i < len(data_lengths):
r = random.random()
b = random.random()
g = random.random()
color = (r, g, b)
figure = plt.Figure(figsize=(4, 5), dpi=100)
ax = figure.add_subplot(111)
ax.set_title("Lengths of packets in " + protocols[i] + " protocol")
line = FigureCanvasTkAgg(figure, root)
line = line.get_tk_widget()
line.grid(row=5, column=i)
line_graphs.append(line)
data = {
'Indices': range(0, len(data_lengths[i])),
'Data lengths': data_lengths[i]
}
data_frame = DataFrame(data, columns=['Indices', 'Data lengths'])
data_frame = data_frame[['Indices',
'Data lengths']].groupby('Indices').sum()
data_frame.plot(kind='line', legend=True, ax=ax, color=color)
i += 1
return line_graphs
def __init__(self, *args, **kwargs):
tk.Tk.__init__(self, *args, **kwargs)
global window
window = self
for button in buttons:
row, column, text, press, release = button
b = ttk.Button(self, text=text)
b.bind("<ButtonPress-1>",
(lambda press: (lambda event: press()))(press))
b.bind("<ButtonRelease-1>",
(lambda release: (lambda event: release()))(release))
b.grid(row=row, column=column)
for checkbox in checkboxes:
row, column, text, command = checkbox
variable = tk.IntVar()
checkbox_variables.append(variable)
ttk.Checkbutton(self,
text=text,
variable=variable,
command=command).grid(row=row, column=column)
for radio_button_group in radio_button_groups:
radio_buttons, command = radio_button_group
variable = tk.IntVar()
radio_button_variables.append(variable)
for radio_button in radio_buttons:
row, column, text, value = radio_button
ttk.Radiobutton(self,
text=text,
variable=variable,
value=value,
command=command).grid(row=row, column=column)
for message in messages:
row, column, columnspan = message
variable = tk.StringVar()
message_variables.append(variable)
m = tk.Label(self)
m.config(font=("Verdana", 14), textvariable=variable)
m.grid(row=row, column=column, columnspan=columnspan)
global canvas
if use_matplotlib:
canvas = FigureCanvasTkAgg(figure, self)
if fixed_size:
axes.set_xlim(0, 1)
axes.set_ylim(0, 1)
canvas.show()
if click_command:
canvas.mpl_connect('button_press_event',
lambda event: click_command(event.xdata,
event.ydata))
canvas.get_tk_widget().grid(row=button_rows,
columnspan=button_columns)
else:
canvas = tk.Canvas(self, width=window_width, height=window_height)
canvas.grid(row=button_rows, columnspan=button_columns)
self.bind("<Control-c>", lambda event: done())
self.bind("<Escape>", lambda event: done())
def plot_bar_graph(dictionary, key_title, value_title, title):
lists = sorted(dictionary.items())
x, y = zip(*lists)
data = {key_title: x, value_title: y}
data_frame = DataFrame(data, columns=[key_title, value_title])
figure = plt.Figure(figsize=(5, 4), dpi=100)
ax = figure.add_subplot(111)
ax.set_title(title)
bar = FigureCanvasTkAgg(figure, root)
bar = bar.get_tk_widget()
bar.grid(row=4, column=1)
df = data_frame[[key_title, value_title]].groupby(key_title).sum()
df.plot(kind='bar', legend=True, ax=ax)
return bar
class Main(MainFrame):
def content(self, master):
# self.button = tk.Button(
# master,
# text = "Run attack (running run.sh)",
# command = self.on_click_hello
# )
# self.button.pack(padx=2, pady=2, fill=tk.X)
'''Initializing the console inside a scrollbar area'''
self.console =
'''Initializing and displaying graph inside a canvas'''
self.canvas = FigureCanvasTkAgg(calc_and_parse_graph(), master=self.parent) # A tk.DrawingArea.
self.canvas.draw()
self.canvas.grid(column=0, row=0, colspan=2, rowspan=2)
self.canvas.get_tk_widget().pack(side=tk.TOP, fill=tk.BOTH, expand=1)
#self.canvas.toolbar = NavigationToolbar2Tk(self.canvas, self.parent)
#self.canvas.toolbar.update()
def on_click_hello(self):
print("hello world!")
def __init__(self, parent, controller):
tk.Frame.__init__(self, parent)
self.controller = controller
name = self.controller.currentResultFolder
if name != "abc":
cur_dir_path = os.path.dirname(os.path.realpath(__file__))
path = Path(cur_dir_path)
path = path.parent.parent
reference = os.path.join(
path,
os.path.join('ZZoutput',
os.path.join(name, 'results_' + name + '.txt')))
if controller.justEnteredViewParameter == 1:
with open(reference) as ff:
dataRef = json.load(ff)
controller.dataRef = dataRef
controller.justEnteredViewParameter = 0
else:
dataRef = controller.dataRef
nbWellsRef = len(dataRef["wellPoissMouv"])
numWell = self.controller.numWell
numPoiss = self.controller.numPoiss
numMouv = self.controller.numMouv
nbWells = len(dataRef["wellPoissMouv"])
if numWell >= nbWells:
if nbWells == 0:
numWell = 0
else:
numWell = nbWells - 1
nbPoiss = len(dataRef["wellPoissMouv"][numWell])
if numPoiss >= nbPoiss:
if nbPoiss == 0:
numPoiss = 0
else:
numPoiss = nbPoiss - 1
nbMouv = len(dataRef["wellPoissMouv"][numWell][numPoiss])
if numMouv >= nbMouv:
if nbMouv == 0:
numMouv = 0
else:
numMouv = nbMouv - 1
label = tk.Label(self, text=" ", font=LARGE_FONT)
label.grid(row=1, column=6)
ttk.Button(self,
text="View video for all wells together",
command=lambda: controller.showValidationVideo(
-1, 0, -1)).grid(row=1, column=1)
# ttk.Button(self, text="Verify wells detection", command=lambda: controller.showValidationVideo(-1,0,-1)).grid(row=1,column=2, columnspan=2)
label = tk.Label(self,
text=name,
font="bold",
justify=LEFT,
pady=10)
label.grid(sticky=W, row=0, column=0, columnspan=8)
label = tk.Label(self, text="Well number:")
label.grid(row=2, column=1)
e1 = tk.Entry(self)
e1.insert(0, numWell)
e1.grid(row=2, column=2)
tk.Button(self,
text="-",
command=lambda: controller.printSomeResults(
int(e1.get()) - 1, e2.get(), e3.get())).grid(
row=2, column=3)
tk.Button(self,
text="+",
command=lambda: controller.printSomeResults(
int(e1.get()) + 1, e2.get(), e3.get())).grid(
row=2, column=4)
ttk.Button(self,
text="View zoomed video for well " + str(numWell),
command=lambda: controller.showValidationVideo(
e1.get(), 1, -1)).grid(row=3, column=2)
def callback(url):
webbrowser.open_new(url)
link1 = tk.Button(self,
text="Video viewing tips",
cursor="hand2",
bg='red')
link1.grid(row=3, column=4)
link1.bind(
"<Button-1>", lambda e: callback(
"https://zebrazoom.org/validationVideoReading.html"))
label = tk.Label(self, text="Fish number:")
label.grid(row=4, column=1)
e2 = tk.Entry(self)
e2.insert(0, numPoiss)
e2.grid(row=4, column=2)
tk.Button(self,
text="-",
command=lambda: controller.printSomeResults(
e1.get(),
int(e2.get()) - 1, e3.get())).grid(row=4, column=3)
tk.Button(self,
text="+",
command=lambda: controller.printSomeResults(
e1.get(),
int(e2.get()) + 1, e3.get())).grid(row=4, column=4)
label = tk.Label(self, text="Bout number:")
label.grid(row=5, column=1)
e3 = tk.Entry(self)
e3.insert(0, numMouv)
e3.grid(row=5, column=2)
tk.Button(self,
text="-",
command=lambda: controller.printSomeResults(
e1.get(), e2.get(),
int(e3.get()) - 1)).grid(row=5, column=3)
tk.Button(self,
text="+",
command=lambda: controller.printSomeResults(
e1.get(), e2.get(),
int(e3.get()) + 1)).grid(row=5, column=4)
button1 = ttk.Button(self,
text="View bout's angle",
command=lambda: controller.printSomeResults(
e1.get(), e2.get(), e3.get()))
button1.grid(row=6, column=2)
if (len(dataRef["wellPoissMouv"][numWell][numPoiss]) > 0):
if ("flag" in dataRef["wellPoissMouv"][numWell][numPoiss]
[numMouv]):
if (dataRef["wellPoissMouv"][numWell][numPoiss][numMouv]
["flag"]):
flagTxt = "UnFlag Movement"
else:
flagTxt = "Flag Movement"
else:
flagTxt = "Flag Movement"
button3 = tk.Button(self,
text=flagTxt,
command=lambda: controller.flagMove(
e1.get(), e2.get(), e3.get()))
if flagTxt == "UnFlag Movement":
button3.configure(bg='red')
button3.grid(row=6, column=4)
prev = ttk.Button(
self,
text="Previous Bout",
command=lambda: controller.printPreviousResults(
e1.get(), e2.get(), e3.get(), nbWells, nbPoiss, nbMouv))
prev.grid(row=7, column=1)
next = ttk.Button(
self,
text="Next Bout",
command=lambda: controller.printNextResults(
e1.get(), e2.get(), e3.get(), nbWells, nbPoiss, nbMouv))
next.grid(row=7, column=2)
tk.Button(self,
text="Go to the previous page",
command=lambda: controller.show_frame(
"ResultsVisualization")).grid(row=8, column=1)
tk.Button(self,
text="Change Right Side Plot",
command=lambda: controller.printSomeResults(
e1.get(), e2.get(), e3.get(), True),
bg="light green").grid(row=8, column=2, columnspan=2)
if (controller.superstructmodified == 1):
button1 = tk.Button(self,
text="Save SuperStruct",
command=lambda: controller.saveSuperStruct(
e1.get(), e2.get(), e3.get()))
button1.configure(bg='orange')
button1.grid(row=7, column=4)
if nbMouv > 0:
begMove = dataRef["wellPoissMouv"][numWell][numPoiss][numMouv][
"BoutStart"]
endMove = dataRef["wellPoissMouv"][numWell][numPoiss][numMouv][
"BoutEnd"]
ttk.Button(self,
text="View video for well " + str(numWell),
command=lambda: controller.showValidationVideo(
e1.get(), 0, begMove)).grid(row=3, column=1)
ttk.Button(self,
text="View bout's video",
command=lambda: controller.showValidationVideo(
e1.get(), 1, begMove)).grid(row=6, column=1)
if controller.visualization == 0 and not (
"TailAngle_smoothed" in dataRef["wellPoissMouv"]
[numWell][numPoiss][numMouv]):
controller.visualization = 1
if controller.visualization == 1 and not (
"TailAngle_Raw" in dataRef["wellPoissMouv"][numWell]
[numPoiss][numMouv]):
controller.visualization = 2
if controller.visualization == 2 and not (
(len(
np.unique(dataRef["wellPoissMouv"][numWell][numPoiss]
[numMouv]["HeadX"])) > 1) and
(len(
np.unique(dataRef["wellPoissMouv"][numWell][numPoiss]
[numMouv]["HeadY"])) > 1)):
controller.visualization = 0
if controller.visualization == 0:
label = tk.Label(
self,
text="Tail Angle Smoothed and amplitudes for well " +
str(numWell) + ", fish " + str(numPoiss) + ", bout " +
str(numMouv),
font=LARGE_FONT)
elif controller.visualization == 1:
label = tk.Label(self,
text="Tail Angle Raw for well " +
str(numWell) + ", fish " + str(numPoiss) +
", bout " + str(numMouv) +
" ",
font=LARGE_FONT)
else:
label = tk.Label(self,
text="Body Coordinates for well " +
str(numWell) + " , fish " +
str(numPoiss) + " , bout " + str(numMouv),
font=LARGE_FONT)
label.grid(row=1, column=7)
if controller.visualization == 0:
tailAngleSmoothed = dataRef["wellPoissMouv"][numWell][
numPoiss][numMouv]["TailAngle_smoothed"].copy()
for ind, val in enumerate(tailAngleSmoothed):
tailAngleSmoothed[ind] = tailAngleSmoothed[ind] * (
180 / (math.pi))
if "Bend_Timing" in dataRef["wellPoissMouv"][numWell][
numPoiss][numMouv]:
freqX = dataRef["wellPoissMouv"][numWell][numPoiss][
numMouv]["Bend_Timing"]
freqY = dataRef["wellPoissMouv"][numWell][numPoiss][
numMouv]["Bend_Amplitude"]
else:
freqX = []
freqY = []
if type(freqY) == int or type(freqY) == float:
freqY = freqY * (180 / (math.pi))
else:
if "Bend_Timing" in dataRef["wellPoissMouv"][numWell][
numPoiss][numMouv]:
freqX = dataRef["wellPoissMouv"][numWell][
numPoiss][numMouv]["Bend_Timing"].copy()
freqY = dataRef["wellPoissMouv"][numWell][
numPoiss][numMouv]["Bend_Amplitude"].copy()
else:
freqX = []
freqY = []
for ind, val in enumerate(freqY):
freqY[ind] = freqY[ind] * (180 / (math.pi))
fx = [begMove]
fy = [0]
if (type(freqX) is int) or (type(freqX) is float):
freqX = [freqX]
freqY = [freqY]
for idx, x in enumerate(freqX):
idx2 = idx - 1
fx.append(freqX[idx2] - 1 + begMove)
fx.append(freqX[idx2] - 1 + begMove)
fx.append(freqX[idx2] - 1 + begMove)
fy.append(0)
fy.append(freqY[idx2])
fy.append(0)
f = Figure(figsize=(5, 5), dpi=100)
a = f.add_subplot(111)
if len(tailAngleSmoothed):
a.plot([i for i in range(begMove, endMove + 1)],
tailAngleSmoothed)
a.plot(fx, fy)
a.plot([i for i in range(begMove, endMove + 1)],
[0 for i in range(0, len(tailAngleSmoothed))])
elif controller.visualization == 1:
tailAngleSmoothed = dataRef["wellPoissMouv"][numWell][
numPoiss][numMouv]["TailAngle_Raw"].copy()
for ind, val in enumerate(tailAngleSmoothed):
tailAngleSmoothed[ind] = tailAngleSmoothed[ind] * (
180 / (math.pi))
f = Figure(figsize=(5, 5), dpi=100)
a = f.add_subplot(111)
a.plot([i for i in range(begMove, endMove + 1)],
tailAngleSmoothed)
a.plot([i for i in range(begMove, endMove + 1)],
[0 for i in range(0, len(tailAngleSmoothed))])
else:
headX = dataRef["wellPoissMouv"][numWell][numPoiss][
numMouv]["HeadX"].copy()
headY = dataRef["wellPoissMouv"][numWell][numPoiss][
numMouv]["HeadY"].copy()
f = Figure(figsize=(5, 5), dpi=100)
a = f.add_subplot(111)
a.plot(headX, headY)
canvas = FigureCanvasTkAgg(f, self)
canvas.draw()
canvas.get_tk_widget().grid(row=2, column=7, rowspan=7)
else:
tailAngleSmoothed = [i for i in range(0, 1)]
f = Figure(figsize=(5, 5), dpi=100)
a = f.add_subplot(111)
a.plot([i for i in range(0, len(tailAngleSmoothed))],
tailAngleSmoothed)
canvas = FigureCanvasTkAgg(f, self)
canvas.draw()
canvas.get_tk_widget().grid(row=2, column=7, rowspan=7)
canvas = Canvas(self)
canvas.create_text(100,
10,
text="No bout detected for well " +
str(numWell))
canvas.grid(row=2, column=7, rowspan=7)
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 BaseTab(ttk.Frame, ABC):
def __init__(self, master=None, **kw):
super().__init__(master=master, **kw)
self.graph = None
@abstractmethod
def add_menu(self):
pass
def add_vertical_separator(self, column):
ttk.Separator(self, orient='vertical')\
.grid(row=0, column=column, pady=5, sticky='NS')
def add_text_frame(self, row, column):
frame = ScrollableFrame(self)
frame.grid(row=row, column=column, sticky='NSWE')
frame.grid_propagate(False)
self.result = InfoLabel(frame.scrollable_frame, font=("Helvetica", 16))
self.result.grid(row=1, column=0)
frame.bind_vertical_scroll('<MouseWheel>', self)
frame.bind_horizontal_scroll('<MouseWheel>', frame.scrollbar_x)
def add_canvas(self, row, column, for_networkX=False):
frame = ttk.Frame(self)
frame.grid(row=row, column=column, sticky='NSWE')
frame.grid_propagate(False)
if not for_networkX:
self.canvas = ResizingSquareCanvas(frame, width=1, height=1)
self.canvas.grid(row=0, column=0)
else:
class CustomToolbar(NavigationToolbar2Tk):
# only display the buttons we need
toolitems = [
t for t in NavigationToolbar2Tk.toolitems
if t[0] in ('Home', 'Pan', 'Zoom', 'Save')
]
figure = Figure(figsize=(5, 4),
constrained_layout=True,
frameon=False)
self.axis = figure.add_subplot(111)
self.axis.axis(False)
self.canvas = FigureCanvasTkAgg(figure, master=frame)
self.toolbar = CustomToolbar(self.canvas, frame)
self.toolbar.update()
self.canvas.get_tk_widget().pack(side=tk.TOP,
fill=tk.BOTH,
expand=True)
self.canvas.draw()
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
def draw_graph(self):
pass
def clear_graph(self):
self.graph = None
self.canvas.delete('all')
def print_graph(self):
if self.graph is not None:
self.result.show_normal(str(self.graph))
def clear_text(self):
self.result.clear()
def append_text(self, text):
self.result.append(text)
class ImageSession:
def __init__(self, master, filename, hdu=0):
# filename should be a string!
self.filename = filename
self.hdu = hdu
# The master window?
self.master = master
if not os.path.exists(self.filename):
tkMessageBox.showerror("File not found", "File {0} doesn't exist!".format(file))
return
self.openFile()
self.createWindow()
def openFile(self):
# Try to open the file and read in the data from HDU
try:
hdulist = pf.open(self.filename)
try:
if hdulist[self.hdu].header['XTENSION'] == 'BINTABLE':
tkMessageBox.showerror("HDU Error", "The HDU {0} is not an ImageHDU!".format(self.hdu))
raise util.NotAnImageHDUError("The HDU {0} is not an ImageHDU!".format(self.hdu))
# HDU is a table -- throw an error!
except KeyError:
# HDU is an image, carry on!
pass
self.rawData = hdulist[self.hdu].data
self.rawData.shape
except IOError:
tkMessageBox.showerror("FITS file error ", "File {0} does not appear to be a valid FITS file!".format(self.filename))
raise util.ImageSessionError("File {0} does not appear to be a valid FITS file!".format(self.filename))
except AttributeError:
tkMessageBox.showerror("FITS file error ", "File {0} does not appear to have data in HDU 0.".format(self.filename))
raise util.ImageSessionError("File {0} does not appear to have data in HDU 0.".format(self.filename))
def createWindow(self):
# Create the actual window to draw the image and scale controls
self.ImageWindow = Tk.Toplevel(self.master)
self.ImageWindow.title(self.filename)
#self.ImageWindow.protocol("WM_DELETE_WINDOW", self.closeImage)
# TODO: THIS SHOULD DETECT SCREEN RESOLUTION
screenSize = (1050/1.5, 1680/1.5)
if self.rawData.shape[0] > screenSize[0] and self.rawData.shape[1] > screenSize[1]:
factor1 = screenSize[0] / self.rawData.shape[0]
factor2 = screenSize[1] / self.rawData.shape[1]
self.zoomFactor = min([factor1, factor2])
elif self.rawData.shape[1] > screenSize[0]:
self.zoomFactor = screenSize[0]/ self.rawData.shape[1]
elif self.rawData.shape[0] > screenSize[1]:
self.zoomFactor = screenSize[1] / self.rawData.shape[0]
else:
self.zoomFactor = 1.
# Create the image tools
scaleTypeLabel = Tk.Label(self.ImageWindow, text="Scaling: ")
scaleTypeLabel.grid(row=0, column=0)
self.scalingName = Tk.StringVar()
self.scalingName.set("arcsinh")
self.scalingOption = Tk.OptionMenu(self.ImageWindow, self.scalingName, "arcsinh","linear","sqrt", command=self.setRescaler)
self.scalingOption.grid(row=0, column=1)
rescaleLabel = Tk.Label(self.ImageWindow, text="Rescale: ")
rescaleLabel.grid(row=1, column=0)
self.scaleValue = Tk.Scale(self.ImageWindow, from_=-4, to=6, resolution=0.05, orient=Tk.HORIZONTAL, showvalue=1, length=300)
self.scaleValue.set(1.0)
self.scaleValue.grid(row=1, column=1)
minLabel = Tk.Label(self.ImageWindow, text="Min Pixel Value: ")
minLabel.grid(row=2, column=0)
self.minValue = Tk.Scale(self.ImageWindow, resolution=0.05, orient=Tk.HORIZONTAL, showvalue=1, length=300)
self.minValue.set(1.0)
self.minValue.grid(row=2, column=1)
maxLabel = Tk.Label(self.ImageWindow, text="Max Pixel Value: ")
maxLabel.grid(row=3, column=0)
self.maxValue = Tk.Scale(self.ImageWindow, resolution=0.05, orient=Tk.HORIZONTAL, showvalue=1, length=300)
self.maxValue.set(1.0)
self.maxValue.grid(row=3, column=1)
# Set the min/max slider boundaries
self.minValue.config(from_=self.rawData.min(), to=self.rawData.max())
self.minValue.set(self.rawData.min())
self.maxValue.config(from_=self.rawData.min(), to=self.rawData.max())
self.maxValue.set(self.rawData.max())
# Set the default rescaler
self.rescaler = util.arcsinhStretch
self.scaleImage()
self.drawImage()
# Bind the sliders to the scaleImage() method
self.scaleValue.bind("<ButtonRelease-1>", self.redraw)
self.minValue.bind("<ButtonRelease-1>", self.redraw)
self.maxValue.bind("<ButtonRelease-1>", self.redraw)
self.scalingOption.bind("<ButtonRelease-1>", self.redraw)
def setRescaler(self, event):
self.rescaler = scalingTypes[self.scalingName.get()]
def redraw(self, event=None):
""" This rescales and redraws the image using the current values for scaling """
self.scaleImage()
self.drawImage()
def updateThumbnail(self, event):
""" """
self.lastMousePosition = (event.x, event.y)
self.pilThumbnail = self.pilImage.transform(self.pilImage.size, Image.EXTENT, (event.x-25,event.y-25,event.x+25,event.y+25))
self.thumbnailImage = ImageTk.PhotoImage(self.pilThumbnail.resize((200,200)))
self.thumbnailImageLabel.configure(image=self.thumbnailImage)
def scaleImage(self):
""" This method re-scales the image data """
self.scaledData = 255.0*self.rescaler(self.rawData, beta=10.**self.scaleValue.get(), min=self.minValue.get(), max=self.maxValue.get(), clip=True)
def plotContour(self, event):
""" If the 'c' key is pressed, generate a contour plot of whatever is in the thumbnail zoom box """
self.contourPlot = Tk.Toplevel(self.master)
self.contourPlot.title("Contour plot for: {0}".format(self.filename))
rawShape = self.rawData.shape
lastx, lasty = self.lastMousePosition
lastx = round(lastx/self.zoomFactor)
lasty = round(lasty/self.zoomFactor)
boxHalfSize = 25/self.zoomFactor
x1,y1,x2,y2 = [x for x in map(round, (lastx-boxHalfSize,lasty-boxHalfSize,lastx+boxHalfSize,lasty+boxHalfSize))]
if x1 < 0:
x1 = 0
x2 = boxHalfSize*2
if x2 > rawShape[1]:
x2 = rawShape[1]
x1 = x2 - boxHalfSize*2
if y1 < 0:
y1 = 0
y2 = boxHalfSize*2
if y2 > rawShape[0]:
y2 = rawShape[0]
y1 = y2 - boxHalfSize*2
thumbData = self.rawData[y1:y2, x1:x2]
shp = thumbData.shape
x,y = np.meshgrid(range(shp[0]), range(shp[1]))
self.fig = Figure(figsize=(5,5))
ax = self.fig.add_subplot(111)
ax.contour(x, y, thumbData)
ax.set_ylim(ax.get_ylim()[::-1])
ax.get_xaxis().set_ticks([])
ax.get_yaxis().set_ticks([])
self.canvas = FigureCanvasTkAgg(self.fig, master=self.contourPlot)
self.canvas.get_tk_widget().pack(side='top', fill='both', expand=1)
def drawImage(self):
""" This method will draw the image into a PhotoImage object in the new image window """
self.pilImage = Image.fromarray(self.scaledData.astype(np.uint8))
newSize = (int(self.pilImage.size[0]*self.zoomFactor), int(self.pilImage.size[1]*self.zoomFactor))
self.pilImage = self.pilImage.resize(newSize)
self.tkImage = ImageTk.PhotoImage(self.pilImage)
self.canvas = Tk.Canvas(self.ImageWindow, width=newSize[0], height=newSize[1], bd=0)
self.canvas.create_image(0, 0, image=self.tkImage, anchor="nw")
self.canvas.grid(row=0, column=2, rowspan=5, sticky="nswe")
self.canvas.bind("<Motion>", self.updateThumbnail)
self.canvas.bind("c", self.plotContour)
self.canvas.focus_set()
""" # Code for source detection:
numSigma = 2.
labels, num = snd.label(self.rawData > (numSigma*np.std(self.rawData)), np.ones((3,3)))
coords = snd.center_of_mass(self.rawData, labels, range(1,num+1))
rad = 5.
for coord in coords:
y,x = coord
x = x*self.zoomFactor
y = y*self.zoomFactor
circ1 = self.canvas.create_oval(x-rad,y-rad,x+rad,y+rad, outline='red')
"""
self.pilThumbnail = self.pilImage.transform(self.pilImage.size, Image.EXTENT, (0,0,50,50))
self.pilThumbnail = self.pilThumbnail.resize((200,200))
self.thumbnailImage = ImageTk.PhotoImage(self.pilThumbnail)
self.thumbnailImageLabel = Tk.Label(self.ImageWindow, image=self.thumbnailImage, command=None)
self.thumbnailImageLabel.grid(row=4, column=0, columnspan=2, rowspan=5)
def start(m_text_initial, p_text_initial, nfd_text_initial, pfd_text_initial,
S_text_initial, explain_initial, options, solver_name,
time_limit):
matplotlib.use("TkAgg")
root = tk.Tk()
actions_lookup = []
def quit():
# Close matplotlib figure so program is not left hanging
plt.close('all')
root.quit()
def random_problem():
# Generate random problem
m_text, p_text, nfd_text, pfd_text = interface.random_problem()
# Set textboxes
spinbox_set(m_spinbox, m_text)
textbox_set(p_textbox, p_text)
textbox_set(nfd_textbox, nfd_text)
textbox_set(pfd_textbox, pfd_text)
def load_problem():
# Locate file
filename = tk.filedialog.askopenfilename(title='Open problem',
filetypes=[('Problem files', '*.problem'), ('Any files', '*')])
# Handle closed dialog
if not filename:
return
# Read file
success, texts = interface.load_problem(filename)
if success:
[m_text, p_text, nfd_text, pfd_text] = texts
spinbox_set(m_spinbox, m_text)
textbox_set(p_textbox, p_text)
textbox_set(nfd_textbox, nfd_text)
textbox_set(pfd_textbox, pfd_text)
else:
E_listbox_set(texts)
def save_problem():
# Locate file
filename = tk.filedialog.asksaveasfilename(title='Save problem as',
filetypes=[('Problem files', '*.problem'), ('Any files', '*')])
# Handle closed dialog
if not filename:
return
# Write file
success, error = interface.save_problem(
filename,
m_spinbox.get(),
textbox_get(p_textbox),
textbox_get(nfd_textbox),
textbox_get(pfd_textbox))
if not success:
E_listbox_set(error)
def optimal_schedule():
# Generate schedule
success, text = interface.optimal_schedule(
m_spinbox.get(),
textbox_get(p_textbox),
textbox_get(nfd_textbox),
textbox_get(pfd_textbox),
solver_name,
time_limit)
if success:
textbox_set(S_textbox, text)
else:
E_listbox_set(text)
def random_schedule():
# Generate schedule
success, text = interface.random_schedule(
m_spinbox.get(),
textbox_get(p_textbox),
textbox_get(nfd_textbox),
textbox_get(pfd_textbox))
if success:
textbox_set(S_textbox, text)
else:
E_listbox_set(text)
def load_schedule():
# Locate file
filename = tk.filedialog.askopenfilename(title='Open schedule',
filetypes=[('Schedule files', '*.schedule'), ('Any files', '*')])
# Handle closed dialog
if not filename:
return
# Read file
success, text = interface.load_text(filename)
if success:
textbox_set(S_textbox, text)
else:
E_listbox_set(text)
def save_file(text, title, filetypes):
# Locate file
filename = tk.filedialog.asksaveasfilename(title=title,
filetypes=filetypes)
# Handle closed dialog
if not filename:
return
# Write file
success, error = interface.save_text(filename, text)
if not success:
E_listbox_set(error)
def save_schedule():
save_file(textbox_get(S_textbox), 'Save schedule as',
[('Schedule files', '*.schedule'), ('Any files', '*')])
def explain(options=options):
success, result = interface.explain(
m_spinbox.get(),
textbox_get(p_textbox),
textbox_get(nfd_textbox),
textbox_get(pfd_textbox),
textbox_get(S_textbox),
options)
if success:
# Setup reasons
E_listbox_set([reason for reason, _ in result])
# Updates actions
nonlocal actions_lookup
actions_lookup = [actions for _, actions in result]
# Select first appliable reason
for index, (_, actions) in enumerate(result):
if actions:
E_listbox.select_set(index)
on_select_reason()
break
fig.canvas.draw()
else:
E_listbox_set(result)
def save_explanation():
save_file(listbox_get(E_listbox), 'Save output as',
[('Text files', '*.txt'), ('Any files', '*')])
# Set E_listbox's items while clearing actions
def E_listbox_set(lines):
actions_lookup = []
listbox_set(E_listbox, lines)
listbox_set(action_listbox, [])
# Shows suggested actions for a selected reason
def on_select_reason(_=None):
# If anything has been explained
if actions_lookup:
# Show suggested actions
readable_actions = actions_lookup[E_listbox.curselection()[0]]
actions = [action for action, _ in readable_actions]
listbox_set(action_listbox, actions)
# Select if possible
if actions:
action_listbox.select_set(0)
# Apply selected action to schedule
def apply(_=None):
# If action is selected
indices = list(action_listbox.curselection())
if indices:
# Find internal representation of action
action_index = indices[0]
reason_index = E_listbox.curselection()[0]
_, action = actions_lookup[reason_index][action_index]
# Apply action
success, result = interface.apply(
m_spinbox.get(),
textbox_get(p_textbox),
textbox_get(nfd_textbox),
textbox_get(pfd_textbox),
textbox_get(S_textbox),
action,
options)
if success:
# Unpack results
nfd_text, pfd_text, S_text = result
# Update textboxes
textbox_set(nfd_textbox, nfd_text)
textbox_set(pfd_textbox, pfd_text)
textbox_set(S_textbox, S_text)
# Automate next step, but do not draw again for explanation
draw_options = dict(options)
draw_options['graphical'] = False
explain(draw_options)
else:
E_listbox_set([result])
# When tab is pressed
def focus_next_window(event):
event.widget.tk_focusNext().focus()
return('break')
root.protocol('WM_DELETE_WINDOW', quit)
root.title('Schedule Explainer')
input_textbox_width = 30
# Create widgets
left_frame = tk.Frame(root)
problem_frame = tk.LabelFrame(left_frame, text='Problem')
problem_command_frame = tk.Frame(problem_frame)
random_problem_button = tk.Button(problem_command_frame, text='Randomise', command=random_problem)
load_problem_button = tk.Button(problem_command_frame, text='Load', command=load_problem)
save_problem_button = tk.Button(problem_command_frame, text='Save', command=save_problem)
m_label = tk.Label(problem_frame, text='Number of machines', anchor=tk.E)
m_spinbox = tk.Spinbox(problem_frame, from_=0, to_=tk.sys.maxsize)
p_label = tk.Label(problem_frame, text='Processing times', anchor=tk.E)
p_textbox = tk.Text(problem_frame, height=3, width=input_textbox_width)
p_scrollbar = attach_scrollbar(problem_frame, p_textbox)
p_textbox.bind('<Tab>', focus_next_window)
nfd_label = tk.Label(problem_frame, text='Negative fixed decisions', anchor=tk.E)
nfd_textbox = tk.Text(problem_frame, height=3, width=input_textbox_width)
nfd_scrollbar = attach_scrollbar(problem_frame, nfd_textbox)
nfd_textbox.bind('<Tab>', focus_next_window)
pfd_label = tk.Label(problem_frame, text='Positive fixed decisions', anchor=tk.E)
pfd_textbox = tk.Text(problem_frame, height=3, width=input_textbox_width)
pfd_scrollbar = attach_scrollbar(problem_frame, pfd_textbox)
pfd_textbox.bind('<Tab>', focus_next_window)
S_frame = tk.LabelFrame(left_frame, text='Schedule')
S_command_frame = tk.Frame(S_frame)
S_optimal_schedule_button = tk.Button(S_command_frame, text='Optimise', command=optimal_schedule)
S_random_button = tk.Button(S_command_frame, text='Randomise', command=random_schedule)
load_S_button = tk.Button(S_command_frame, text='Load', command=load_schedule)
save_S_button = tk.Button(S_command_frame, text='Save', command=save_schedule)
S_textbox = tk.Text(S_frame, height=3, width=input_textbox_width)
S_textbox.bind('<Tab>', focus_next_window)
S_scrollbar = attach_scrollbar(S_frame, S_textbox)
explain_button = tk.Button(S_frame, text='Explain', command=explain)
right_frame = tk.Frame(root)
fig = plt.figure(0)
S_figure = FigureCanvasTkAgg(fig, master=right_frame).get_tk_widget()
E_frame = tk.LabelFrame(right_frame, text='Explanation')
E_listbox = tk.Listbox(E_frame, exportselection=False)
E_listbox.bind('<<ListboxSelect>>', on_select_reason)
E_listbox.bind('<Return>', apply)
E_scrollbar = attach_scrollbar(E_frame, E_listbox)
save_E_button = tk.Button(E_frame, text='Save', command=save_explanation)
action_frame = tk.LabelFrame(right_frame, text='Actions')
action_listbox = tk.Listbox(action_frame)
action_listbox.bind('<Return>', apply)
action_scrollbar = attach_scrollbar(action_frame, action_listbox)
apply_action_button = tk.Button(action_frame, text='Apply', command=apply)
# Geometry
padding = 8
h_fill = tk.W + tk.E
v_fill = tk.N + tk.S
fill = h_fill + v_fill
root.geometry("1280x720")
root.rowconfigure(0, weight=1)
root.columnconfigure(1, weight=1)
left_frame.grid(row=0, column=0, sticky=v_fill)
left_frame.rowconfigure(0, weight=1)
left_frame.rowconfigure(1, weight=1)
problem_frame.grid(row=0, column=0, padx=padding, pady=padding, sticky=v_fill)
problem_command_frame.grid(row=0, column=0, columnspan=3, padx=padding, pady=padding, sticky=h_fill)
problem_command_frame.columnconfigure(0, weight=1)
problem_command_frame.columnconfigure(1, weight=1)
problem_command_frame.columnconfigure(2, weight=1)
random_problem_button.grid(row=0, column=0, sticky=h_fill)
load_problem_button.grid(row=0, column=1, padx=padding, sticky=h_fill)
save_problem_button.grid(row=0, column=2, sticky=h_fill)
problem_frame.rowconfigure(2, weight=1)
problem_frame.rowconfigure(3, weight=1)
problem_frame.rowconfigure(4, weight=1)
m_label.grid(row=1, column=0, padx=padding, sticky=h_fill)
m_spinbox.grid(row=1, column=1, columnspan=2, padx=(0, padding), sticky=h_fill)
p_label.grid(row=2, column=0, padx=padding, pady=padding, sticky=h_fill)
p_textbox.grid(row=2, column=1, pady=padding, sticky=v_fill)
p_scrollbar.grid(row=2, column=2, padx=(0, padding), pady=padding, sticky=v_fill)
nfd_label.grid(row=3, column=0, padx=padding, sticky=h_fill)
nfd_textbox.grid(row=3, column=1, sticky=v_fill)
nfd_scrollbar.grid(row=3, column=2, padx=(0, padding), sticky=v_fill)
pfd_label.grid(row=4, column=0, padx=padding, pady=padding, sticky=h_fill)
pfd_textbox.grid(row=4, column=1, pady=padding, sticky=v_fill)
pfd_scrollbar.grid(row=4, column=2, padx=(0, padding), pady=padding, sticky=v_fill)
S_frame.grid(row=1, column=0, padx=padding, pady=(0, padding), ipadx=50, sticky=fill)
S_frame.rowconfigure(1, weight=1)
S_frame.columnconfigure(0, weight=1)
S_command_frame.grid(row=0, column=0, columnspan=2, padx=padding, pady=padding, sticky=h_fill)
S_command_frame.columnconfigure(0, weight=1)
S_command_frame.columnconfigure(1, weight=1)
S_command_frame.columnconfigure(2, weight=1)
S_command_frame.columnconfigure(3, weight=1)
S_optimal_schedule_button.grid(row=0, column=0, padx=(0, padding), sticky=h_fill)
S_random_button.grid(row=0, column=1, padx=(0, padding), sticky=h_fill)
load_S_button.grid(row=0, column=2, padx=(0, padding), sticky=h_fill)
save_S_button.grid(row=0, column=3, sticky=h_fill)
S_textbox.grid(row=1, column=0, padx=(padding, 0), sticky=fill)
S_scrollbar.grid(row=1, column=1, padx=(0, padding), sticky=v_fill)
explain_button.grid(row=2, column=0, columnspan=2, padx=padding, pady=padding, sticky=h_fill)
right_frame.grid(row=0, column=1, sticky=fill)
right_frame.rowconfigure(1, weight=1)
right_frame.columnconfigure(0, weight=1)
right_frame.columnconfigure(1, weight=1)
S_figure.grid(row=0, column=0, columnspan=2, sticky=h_fill, padx=padding, pady=padding)
E_frame.grid(row=1, column=0, sticky=fill, padx=padding, pady=(0, padding))
E_frame.rowconfigure(0, weight=1)
E_frame.columnconfigure(0, weight=1)
E_listbox.grid(row=0, column=0, sticky=fill, padx=(padding, 0), pady=(padding, 0))
E_scrollbar.grid(row=0, column=1, sticky=v_fill, padx=(0, padding), pady=(padding, 0))
save_E_button.grid(row=1, column=0, columnspan=2, padx=padding, pady=padding, sticky=h_fill)
action_frame.grid(row=1, column=1, sticky=fill, padx=padding, pady=(0, padding))
action_frame.rowconfigure(0, weight=1)
action_frame.columnconfigure(0, weight=1)
action_frame.rowconfigure(0, weight=1)
action_listbox.grid(row=0, column=0, sticky=fill, padx=(padding, 0), pady=(padding, 0))
action_scrollbar.grid(row=0, column=1, sticky=v_fill, padx=(0, padding), pady=(padding, 0))
apply_action_button.grid(row=1, column=0, columnspan=2, padx=padding, pady=padding, sticky=h_fill)
# Initial state from command line
spinbox_set(m_spinbox, m_text_initial)
textbox_set(p_textbox, p_text_initial)
textbox_set(nfd_textbox, nfd_text_initial)
textbox_set(pfd_textbox, pfd_text_initial)
textbox_set(S_textbox, S_text_initial)
if explain_initial:
explain()
root.mainloop()
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="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()
def intial(self):
self.note.add(self.tab1,
text="SPI graph") #,image=scheduledimage, compound=TOP)
#self.note.pack()
label = tk.Label(self.tab1, text="Graph Page!")
label.grid(row=1) #,pady=3,padx=3)
exit_btn = tk.Button(self.tab1,
text='Go back to main page',
command=self.close,
activebackground='grey',
activeforeground='#AB78F1',
bg='#58F0AB',
highlightcolor='red',
padx='10px',
pady='3px')
exit_btn.grid(row=2, column=2)
import matplotlib.pyplot as plt
from matplotlib.figure import Figure
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
## fig = Figure(figsize=(7,5), dpi=200)
fig = plt.figure()
num = int("%i11" % len(self.df.columns))
i = 0
ax = []
for col in self.df.columns:
ax1 = fig.add_subplot(num + i)
ax.append(ax1)
spi_pos = self.df[col].clip(lower=0).to_frame(col)
spi_neg = self.df[col].clip(upper=0).to_frame(col)
## print(spi)
self.df[col].plot(ax=ax[i], color="black")
plt.fill_between(spi_neg.index, spi_neg[col].values, color="r")
plt.fill_between(spi_pos.index, spi_pos[col].values, color="b")
ax1.legend(loc='right',
bbox_to_anchor=(1.15, 0.9),
shadow=True,
fontsize=10)
i += 1
#plt.show()
self.frame = ttk.Frame(self.tab1)
self.frame.grid(row=2, sticky=tk.W + tk.E)
canvas = FigureCanvasTkAgg(fig, self.frame)
canvas.draw()
canvas = canvas.get_tk_widget()
canvas.grid(row=1,
column=0,
rowspan=10,
columnspan=4,
sticky=tk.W + tk.E + tk.N + tk.S)
f = []
for col in self.df.columns:
tab = ttk.Frame(self.note)
f.append(tab)
self.note.add(tab, text=col)
df2 = self.df[col].to_frame(col)
df2.dropna(inplace=True)
#print (df2.head())
import statsmodels.api as sm
decomposition = sm.tsa.seasonal_decompose(df2, model='additive')
fig2 = decomposition.plot()
plt.figure(figsize=(15, 5))
self.frame = ttk.Frame(tab)
self.frame.grid(row=2, sticky=tk.W + tk.E)
canvas = FigureCanvasTkAgg(fig2, self.frame)
canvas.draw()
canvas = canvas.get_tk_widget()
canvas.grid(row=1,
column=0,
rowspan=10,
columnspan=4,
sticky=tk.W + tk.E + tk.N + tk.S)
self.tab2 = ttk.Frame(self.note)
self.note.add(self.tab2, text="Frequency")
fig2 = plt.figure()
num = int("%i11" % len(self.df.columns))
i = 0
ax = []
for col in self.df.columns:
ax2 = fig2.add_subplot(num + i)
ax.append(ax2)
SPI = self.df[col].to_frame(col)
SPI.dropna(inplace=True)
print(SPI.head())
SPI["Class"] = SPI[col].apply(reclass)
SPIgroup = SPI.groupby(by="Class")
count = SPIgroup.count()
d = SPIclasses.join(count)
print(d.head())
plt.style.use('ggplot')
color_palette_list = [
'#009ACD', '#ADD8E6', '#63D1F4', '#0EBFE9', '#C1F0F6',
'#0099CC', '#909090'
]
d.plot(kind='barh',
figsize=(12, 7),
color=color_palette_list,
fontsize=6,
ax=ax[i])
#plt.set_title('Amount Frequency of %s'%col)
ax2.set_xlabel('Frequency')
ax2.set_ylabel('Classes')
## rects = fig2.patches
autolabel(ax2, "left")
i += 1
self.frame1 = ttk.Frame(self.tab2)
self.frame1.grid(row=2, sticky=tk.W + tk.E)
canvas = FigureCanvasTkAgg(fig2, self.frame1)
canvas.draw()
canvas = canvas.get_tk_widget()
canvas.grid(row=1,
column=0,
rowspan=10,
columnspan=4,
sticky=tk.W + tk.E + tk.N + tk.S)
##
#print(self.note[col])
## tab_names = []
## for i in self.note.tabs():
## print (i)
## tab_names.append(self.note.tab(i, "text"))
## print (tab_names)
##
####
#### plt.show()
##
##
##
#fig.savefig(out[:-3]+"png")
## a = f.add_subplot(111)
## a.plot([1,2,3,4,5,6,7,8],[5,6,1,3,8,9,3,5])
self.note.pack()
y2 = [i**2 for i in x]
plt.xlabel("x")
plt.ylabel("y")
graf=plt.plot(x,y,x,y2)
#fig=plt.figure()
lbl=FigureCanvasTkAgg(fig,root)
#lbl.get_tk_widget().grid(row=11,column=2,columnspan=10)
lbl.get_tk_widget().grid(column=0,row=9,columnspan=10)
lbl.draw()
FileName=Entry(root,width=30,textvariable=name)
FileName.grid(row=0, column=1, columnspan=3,pady=10)
FileName.insert(0,'img_1.jpg')
lbl = Label(root, text=" X1 ")
lbl.grid(column=0, row=5,pady=10)
txt11 = Entry(root,width=10)
txt11.grid(column=1, row=5,pady=10)
lbl = Label(root, text=" X2 ")
lbl.grid(column=2, row=5,pady=10)
txt12 = Entry(root,width=10)
txt12.grid(column=3, row=5,pady=10)
lbl = Label(root, text=" Y1 ")
lbl.grid(column=0, row=7,pady=10)
txt21 = Entry(root,width=10)
txt21.grid(column=1, row=7,pady=10)
lbl = Label(root, text=" Y2 ")
lbl.grid(column=2, row=7,pady=10)
txt22 = Entry(root,width=10)
txt22.grid(column=3, row=7,pady=10)
render=((img_rows, img_cols))
class GUI():
def __init__(self, tempDir):
self.tempDir = tempDir
self.done = False
self.bg = "#f0f0f0"
self.btnCol = "light grey"
self.files = []
self.scales = [1 for x in range(10)]
self.empty = [True for x in range(10)]
self.data = [0 for x in range(10)]
self.figures = [0 for x in range(10)]
self.views = [-1 for x in range(10)]
self.addresses = [0 for x in range(10)]
self.resultTypes = [0 for x in range(10)]
self.current = 0
def main_menu(self):
#Displays the main menu page
#========== Setup
root = tk.Tk()
root.configure(bg=self.bg)
root.state("zoomed")
h = root.winfo_screenheight()
#========== Weighting
root.rowconfigure(1, weight=1)
root.rowconfigure(3, weight=1)
root.rowconfigure(5, weight=1)
root.rowconfigure(7, weight=1)
root.rowconfigure(9, weight=1)
root.columnconfigure(0, weight=1)
#========== Widgets
#===== Row 0, 1, 2
tk.Frame(root, bg=self.bg, height=round(h * 0.1)).grid(row=0, column=0)
tk.Label(root,
bg=self.bg,
text="Microscope image analyser",
justify="center",
font=("Arial", round(h * 0.06))).grid(row=1, column=0)
tk.Frame(root, bg=self.bg, height=round(h * 0.1)).grid(row=2, column=0)
#===== Row 3, 4
tk.Button(root,
bg=self.btnCol,
text="Image analysis",
justify="center",
font=("Calibri", round(h * 0.03)),
width=30,
command=partial(self.select_file, root,
"Select image to analyse",
("Png files", "*.png"), 0)).grid(row=3,
column=0)
tk.Frame(root, bg=self.bg).grid(row=4, column=0)
#===== Row 5, 6
tk.Button(root,
bg=self.btnCol,
text="Load saved data",
justify="center",
font=("Calibri", round(h * 0.03)),
width=30,
command=partial(self.select_file, root,
"Select results file",
("Text files", "*.txt"), 1)).grid(row=5,
column=0)
tk.Frame(root, bg=self.bg).grid(row=6, column=0)
#===== Row 7, 8
tk.Button(
root,
bg=self.btnCol,
text="View results",
justify="center",
font=("Calibri", round(h * 0.03)),
width=30,
command=lambda: [root.destroy(), self.results()]).grid(row=7,
column=0)
tk.Frame(root, bg=self.bg).grid(row=8, column=0)
#===== Row 9
tk.Button(root,
bg=self.btnCol,
text="Quit",
justify="center",
font=("Calibri", round(h * 0.03)),
width=30,
command=root.destroy).grid(row=9, column=0)
#===== Row 10
tk.Frame(root, height=round(h * 0.2)).grid(row=10, column=0)
#========== Mainloop
root.mainloop()
def plot_histogram(self):
#Creates a figure containing a histogram
fig = Figure()
fig.patch.set_facecolor(self.bg)
plot = fig.gca() #Creates plot for histogram to be on
plot.hist(self.data[self.current], 30) #Plot histogram with 30 bins
plot.yaxis.set_major_locator(
MaxNLocator(integer=True)) #Make ticks integers
plot.set_xlabel("Diameter", fontsize=20) #Set label size
plot.set_ylabel("Frequency", fontsize=20)
plot.tick_params(labelsize=15) #Set tick label size
self.figures[self.current] = fig #Record new figure
def remove_entry(self, index, refresh, root=None):
#Removes an item from the stored results, given the index
def remove(array, index):
#Removes 1 item from a list given its index
return [array[x] for x in range(len(array)) if x != index]
self.files = remove(self.files, index)
self.scales = remove(self.scales, index)
self.scales.append(1)
self.empty = remove(self.empty, index)
self.empty.append(True)
self.data = remove(self.data, index)
self.data.append(0)
self.figures = remove(self.figures, index)
self.figures.append(0)
self.views = remove(self.views, index)
self.views.append(-1)
self.addresses = remove(self.addresses, index)
self.addresses.append(0)
self.resultTypes = remove(self.resultTypes, index)
self.resultTypes.append(0)
if refresh:
if self.current > index:
self.current -= 1
if self.current >= len(self.files) and len(self.files) > 0:
self.current = len(self.files) - 1
root.destroy()
self.results()
def results(self):
#Displays analysis results page
#========== Setup
root = tk.Tk()
root.configure(bg=self.bg)
root.state("zoomed")
w = root.winfo_screenwidth()
h = root.winfo_screenheight()
#========== Weighting / padding
root.rowconfigure(0, pad=h * 0.05)
root.rowconfigure(12, pad=h * 0.05)
root.columnconfigure(1, weight=1)
root.columnconfigure(2, weight=1)
root.columnconfigure(3, weight=1)
root.columnconfigure(4, weight=1)
#========== Widgets
#===== Row 0
tk.Button(
root,
bg=self.btnCol,
text="Main menu",
justify="center",
font=("Calibri", round(h * 0.02)),
command=lambda: [root.destroy(), self.main_menu()]).grid(
row=0, column=0, sticky="NW")
self.resultsTitle = tk.StringVar()
tk.Label(root,
bg=self.bg,
textvariable=self.resultsTitle,
justify="center",
font=("Arial", round(h * 0.04))).grid(row=0,
column=0,
columnspan=6)
#===== Other results
tk.Label(root,
bg=self.bg,
text="Other results:",
justify="left",
font=("Calibri", round(h * 0.03))).grid(row=1, column=5)
self.others = []
for x in range(10):
try:
self.others.append(
tk.Button(root,
bg=self.btnCol,
text=self.files[x],
justify="left",
font=("Calibri", round(h * 0.02)),
width=20,
command=partial(self.set_results, x, root)))
except IndexError:
self.others.append(
tk.Button(root,
bg=self.btnCol,
text="",
justify="left",
font=("Calibri", round(h * 0.02)),
width=20,
command=partial(self.set_results, x, root)))
self.others[x].grid(row=x + 2, column=5)
tk.Button(root,
bg=self.btnCol,
text="X",
justify="center",
font=("Arial", round(h * 0.02)),
width=2,
command=partial(self.remove_entry, x, True,
root)).grid(row=x + 2, column=6)
#===== Row 12
tk.Label(root,
bg=self.bg,
text="Scale:",
font=("Calibri", round(h * 0.03))).grid(row=12,
column=0,
sticky="E")
root.bind("<Return>", partial(self.update_scale, root))
self.scaleEntry = tk.StringVar()
tk.Entry(root,
textvariable=self.scaleEntry,
font=("Calibri", round(h * 0.03)),
width=10).grid(row=12, column=1, sticky="W")
tk.Button(root,
bg=self.btnCol,
text="Original image",
width=15,
font=("Calibri", round(h * 0.03)),
command=partial(self.set_view, root, 1)).grid(row=12,
column=2)
tk.Button(root,
bg=self.btnCol,
text="Analysed image",
width=15,
font=("Calibri", round(h * 0.03)),
command=partial(self.set_view, root, 2)).grid(row=12,
column=3)
tk.Button(root,
bg=self.btnCol,
text="Histogram",
width=15,
font=("Calibri", round(h * 0.03)),
command=partial(self.set_view, root, 0)).grid(row=12,
column=4)
tk.Button(root,
bg=self.btnCol,
text="Save",
width=10,
font=("Calibri", round(h * 0.03)),
command=self.save).grid(row=12, column=5)
self.set_results(self.current, root)
self.set_view(root, 0)
root.mainloop()
def save(self):
#Writes the scale adjusted diameters to txt file in csv format
name = self.files[self.current] #Get shorter identifier
name = name[:name.rindex(".")] + "-results.txt"
address = filedialog.asksaveasfilename(title="Save results file",
initialfile=name,
filetype=(("Text files",
"*.txt"),
("All files", "*.*")))
file = open(address, "w+")
file.write(','.join([str(X) for X in self.data[self.current]]))
file.close(
) #Store diameters including scale adjustment, fstring used so it is 1 argument
def select_file(self, root, title, filetype, resultType):
#Allows the user to select an image file from a directory
file = filedialog.askopenfilename(title=title,
filetypes=(filetype, ("All files",
"*.*")))
if file != "": #If operation not cancelled
self.files.append(file[file.rindex("/") + 1:]) #Get filename only
if len(self.files) > 10: #If list full, replace oldest item
self.remove_entry(0, False)
self.current = 9
self.current = len(self.files) - 1
self.addresses[self.current] = file
self.resultTypes[self.current] = resultType
root.destroy()
if resultType == 0: #Image analysis
pic = image(file, self.tempDir) #Do overall analysis
particles = pic.create_objects() #Do particle analysis
self.data[self.current] = [P.diameter for P in particles]
elif resultType == 1: #Reading results file
text = open(file, "r").read()
self.data[self.current] = text.split(",")
self.data[self.current] = [
float(X) for X in self.data[self.current]
]
self.plot_histogram() #Create histogram figure
self.results()
def set_results(self, new, root):
#Changes to a new set of analysis results
if len(self.files) > new: #If results exist
self.others[self.current].config(
relief="raised") #Deselect previous
self.current = new
self.others[self.current].config(relief="sunken") #select current
self.resultsTitle.set(
f"Results - {self.files[self.current]}") #Change title
if self.empty[self.current]:
self.scaleEntry.set("") #If no scale set don't display scale
else:
self.scaleEntry.set(str(float(self.scales[self.current] *
127))) #Else do display scale
self.set_view(root)
def set_view(self, root, view=None):
#Changes to viewing histogram, original image, or analysed image
w = root.winfo_screenwidth()
h = root.winfo_screenheight()
if self.views[self.current] == 0:
try:
self.histogram.destroy() #Destroy histogram
except Exception:
pass
elif self.views[self.current] == 1 or self.views[
self.current] == 2: #If previous was image
try:
self.picWidget.destroy() #Destroy image
except Exception:
pass
if view != None:
self.views[self.current] = view #Update to new view
if self.views[self.current] == 0:
self.histogram = FigureCanvasTkAgg(
self.figures[self.current],
master=root).get_tk_widget() #Get widget
self.histogram.config(width=round(w * 0.75),
height=round(h * 0.7)) #Resize cavas
self.histogram.grid(row=1, column=0, rowspan=11,
columnspan=5) #Place canvas
elif self.views[self.current] == 1 or self.views[self.current] == 2:
if self.resultTypes[self.current] == 0:
if self.views[self.current] == 1:
file = self.addresses[
self.current] #Get shorter version of file name
pic = ImageTk.PhotoImage(
Image.open(file)) #Get original image
else:
file = self.files[self.current]
file = self.tempDir + "\\" + file[:file.rindex(
'.')] + "-analysed" + file[file.rindex('.'):]
pic = ImageTk.PhotoImage(
Image.open(file)) #Get analysed image
self.picWidget = tk.Label(root,
image=pic,
width=round(w * 0.75),
height=round(h * 0.7)) #Image label
self.picWidget.image = pic #Stops the image being discarded by memory manager
self.picWidget.grid(row=1, column=0, rowspan=11, columnspan=5)
else:
self.views[self.current] = 0
self.set_view(root, 0)
def update_scale(self, root, key):
#Records the scale if it is valid
old = self.scales[self.current]
try:
self.scales[self.current] = float(
self.scaleEntry.get()) / 127 #Get scale
if self.scales[self.current] > 0:
for x in range(len(self.data[
self.current])): #Adjust each item to new scale
self.data[
self.current][x] *= self.scales[self.current] / old
self.plot_histogram() #Replot histogram
self.empty[
self.current] = False #Record that scale has been set
self.set_results(self.current, root) #Redraw canvas
else:
self.scales[self.current] = old
except ValueError:
pass #Unless not valid
class DataAquisitionUI(UserInterface):
def __init__(
self,
layout_path,
data_src=[DummyDataSource()],
vis_data=100
):
super().__init__(layout_path)
self.plt_config = self.ui_config['plot config']
self.running=True
self.collect = False
self.vis_data = vis_data
self.data_src = data_src
self.protocol("WM_DELETE_WINDOW", self.quit_app)
self.init_plot()
self.cleanup()
def init_plot(self):
"""
Sets up plot with colors and formats. Turns on
interactive mode and places the plot in the
grid of the parent.
"""
pltconf = self.plt_config["global config"]
bg_color, fg_color = pltconf['bg'], pltconf['fg']
self.figure, self.ax1 = subplots(facecolor=bg_color)
self.ax2 = self.ax1.twinx()
self.ax1.set_xlabel(pltconf['x label'])
self.ax1.set_ylabel(pltconf['y1 label'])
self.ax2.set_ylabel(pltconf['y2 label'])
self.lines = [self.ax1.add_line(
mlplines.Line2D([], [], label=label, **vals)
) for label, vals in self.plt_config['lines axis 1'].items()
]
self.lines += [self.ax2.add_line(
mlplines.Line2D([], [], label=label, **vals)
) for label, vals in self.plt_config['lines axis 2'].items()
]
for line in self.lines:
line.xdata, line.ydata = [], []
labels = [l.get_label() for l in self.lines]
legend = self.ax2.legend(
self.lines, labels,
loc='upper left',
facecolor=bg_color,
edgecolor=bg_color,
framealpha=1.0
)
for text in legend.get_texts():
text.set_color(fg_color)
for axis in [self.ax1, self.ax2]:
axis.set_facecolor(bg_color)
for side in ['bottom', 'top', 'right', 'left']:
axis.spines[side].set_color(fg_color)
axis.tick_params(axis='x', colors=fg_color)
axis.tick_params(axis='y', colors=fg_color)
axis.yaxis.label.set_color(fg_color)
axis.xaxis.label.set_color(fg_color)
axis.grid(color=fg_color)
axis.set_autoscaley_on(True)
axis.set_autoscalex_on(True)
tight_layout()
ion()
self.data_plot = PltCanvas(self.figure, master=self).get_tk_widget()
self.data_plot.grid(**pltconf['grid'])
def cleanup(self):
"""
Re-initializes the parameters for data collection and clears the
console screen.
"""
for line in self.lines:
line.xdata = []
line.ydata = []
self.data = []
def daq_loop(self):
"""
Part of the mainloop. This function will run every 0.5 seconds. If
the "collect" parameter is set to True it will append the data it
collects to an array to be saved to the output file.
The loop functions with these instructions:
- Get data as a list from some source
- Save the data to an array if self.collect == True
- Update the graph with the latest data point
- Loop
This will execute on startup and continue doing while mainloop is
still running.
"""
data_point = []
for src in self.data_src:
data_point += src.get_data()
if not self.valid_data(data_point):
self.after(0, self.daq_loop)
return
self.process_data(data_point)
if self.collect: self.data_collect(data_point)
self.graph_data(data_point)
if self.running: self.after(0, self.daq_loop)
def graph_data(self, data1):
""" Update the data to be graphed and then update the graph """
for i, line in enumerate(self.lines):
assert len(line.xdata) == len(line.ydata)
if len(line.xdata) > self.vis_data:
line.xdata.pop(0)
line.ydata.pop(0)
line.xdata.append(data1[0])
line.ydata.append(data1[i+1])
line.set_xdata(line.xdata)
line.set_ydata(line.ydata)
self.ax1.relim()
self.ax2.relim()
self.ax1.autoscale_view()
self.ax2.autoscale_view()
self.figure.canvas.draw()
self.figure.canvas.flush_events()
def valid_data(self, data_point):
"""
Check that data is valid and do any preprocessing on the data.
Must return True or False.
"""
print(data_point)
return True
def process_data(self, data_point):
"""
Do any processing needed before data collection and graphing.
"""
pass
def data_collect(data_point):
"""
Processing for data collection.
"""
pass
def quit_app(self, event=None):
"""Safely exits the program."""
if self.collect:
if not askyesno(
"Quit Warning",
"DAQ is still running!\nAre you sure you want to quit?"
):
return
self.running = False
self.destroy()
raise SystemExit
