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Merge pull request #16 from ManuSetty/develop
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Develop
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@ManuSetty
ManuSetty authored Jun 24, 2016
2 parents 0b291ce + 1a39397 commit ec1df6c
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Showing 4 changed files with 106 additions and 6 deletions.
Binary file modified docs/wishbone_tutorial.pptx
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2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@


setup(name='wishbone',
version='0.2.4',
version='0.3',
description='Wishbone algorithm for identifying bifurcating trajectories from single-cell data',
author='Manu Setty',
author_email='manu.setty@columbia.edu',
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2 changes: 1 addition & 1 deletion src/wishbone/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@
from . import wishbone_gui
from . import autocomplete_entry

__version__ = "0.2.4"
__version__ = "0.3"
108 changes: 104 additions & 4 deletions src/wishbone/wishbone_gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,18 @@
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
import matplotlib.pyplot as plt
from matplotlib.figure import Figure
from matplotlib.patches import Rectangle
from matplotlib.path import Path
import wishbone
import os
import sys
import platform
import pandas as pd
import tkinter as tk
import numpy as np
from tkinter import filedialog
import pickle
import random

class wishbone_gui(tk.Tk):
def __init__(self,parent):
Expand Down Expand Up @@ -52,6 +56,7 @@ def initialize(self):
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)

Expand Down Expand Up @@ -123,6 +128,8 @@ def processData(self):
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()
Expand Down Expand Up @@ -164,6 +171,7 @@ def runTSNE(self):

def _runTSNE(self):
self.scdata.run_tsne(n_components=self.nCompVar.get())
self.gates = {}

#enable buttons
self.analysisMenu.entryconfig(2, state='normal')
Expand Down Expand Up @@ -207,6 +215,12 @@ def runWishbone(self):
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)
Expand Down Expand Up @@ -237,8 +251,17 @@ def runWishbone(self):

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())

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')
Expand All @@ -250,6 +273,9 @@ def plotPCA(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.setGateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')

#pop up for # components
self.PCAOptions = tk.Toplevel()
self.PCAOptions.title("PCA Plot Options")
Expand Down Expand Up @@ -281,7 +307,9 @@ def plotTSNE(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')

self.setGateButton.config(state='normal')
self.visMenu.entryconfig(6, state='normal')

self.resetCanvas()
self.fig, self.ax = self.scdata.plot_tsne()
self.canvas = FigureCanvasTkAgg(self.fig, self)
Expand All @@ -293,6 +321,9 @@ def plotDM(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.setGateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')

self.geometry('950x550')

self.resetCanvas()
Expand All @@ -306,7 +337,9 @@ 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)
Expand Down Expand Up @@ -336,7 +369,9 @@ def plotWBOnTsne(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')

self.setGateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')

self.resetCanvas()
self.fig, self.ax = self.wb.plot_wishbone_on_tsne()
self.canvas = FigureCanvasTkAgg(self.fig, self)
Expand All @@ -353,6 +388,9 @@ def plotWBMarkerTrajectory(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.setGateButton.config(state='disabled')
self.visMenu.entryconfig(6, 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)
Expand All @@ -376,6 +414,9 @@ def plotWBHeatMap(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.setGateButton.config(state='disabled')
self.visMenu.entryconfig(6, 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)
Expand All @@ -395,6 +436,9 @@ def plotGeneExpOntSNE(self):
self.saveButton.config(state='normal')
self.component_menu.config(state='disabled')
self.updateButton.config(state='disabled')
self.setGateButton.config(state='disabled')
self.visMenu.entryconfig(6, state='disabled')

self.resetCanvas()
self.fig, self.ax = self.scdata.plot_gene_expression(self.selectedGenes)
self.canvas = FigureCanvasTkAgg(self.fig, self)
Expand Down Expand Up @@ -444,6 +488,62 @@ def savePlot(self):
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:
Expand Down

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