<filename>2_TOT/visualize_pnas.py
# Copyright 2015 <NAME>

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

 
import fileinput
from sets import Set
import random
import scipy.special
import math
import numpy as np
import matplotlib.pyplot as plt
import scipy.stats
from scipy.stats import beta
import pprint, pickle

def VisualizeTopics(phi, words, num_topics, viz_threshold=9e-3):
	phi_viz = np.transpose(phi)
	words_to_display = ~np.all(phi_viz <= viz_threshold, axis=1)
	words_viz = [words[i] for i in range(len(words_to_display)) if words_to_display[i]]
	phi_viz = phi_viz[words_to_display]

	fig, ax = plt.subplots()
	heatmap = plt.pcolor(phi_viz, cmap=plt.cm.Blues, alpha=0.8)
	plt.colorbar()

	#fig.set_size_inches(8, 11)
	ax.grid(False)
	ax.set_frame_on(False)

	ax.set_xticks(np.arange(phi_viz.shape[1]) + 0.5, minor=False)
	ax.set_yticks(np.arange(phi_viz.shape[0]) + 0.5, minor=False)
	ax.invert_yaxis()
	ax.xaxis.tick_top()
	#plt.xticks(rotation=45)
	
	for t in ax.xaxis.get_major_ticks():
	    t.tick1On = False
	    t.tick2On = False
	for t in ax.yaxis.get_major_ticks():
	    t.tick1On = False
	    t.tick2On = False

	column_labels = words_viz	#['Word ' + str(i) for i in range(1,1000)]
	row_labels = ['Topic ' + str(i) for i in range(1,num_topics+1)]
	ax.set_xticklabels(row_labels, minor=False)
	ax.set_yticklabels(column_labels, minor=False)

	plt.show()

def VisualizeEvolution(psi):
	xs = np.linspace(0, 1, num=1000)
	fig, ax = plt.subplots()

	for i in range(len(psi)):
		ys = [math.pow(1-x, psi[i][0]-1) * math.pow(x, psi[i][1]-1) / scipy.special.beta(psi[i][0],psi[i][1]) for x in xs]
		ax.plot(xs, ys, label='Topic ' + str(i+1))

	ax.legend(loc='best', frameon=False)
	plt.show()

def main():
	resultspath = '../results/pnas_tot/'
	tot_pickle_path = resultspath + 'pnas_tot.pickle'

	tot_pickle = open(tot_pickle_path, 'rb')
	par = pickle.load(tot_pickle)
	VisualizeTopics(par['n'], par['word_token'], par['T'])
	VisualizeEvolution(par['psi'])

if __name__ == "__main__":
    main()

<filename>2_TOT/visualize_pnas.py
# Copyright 2015 <NAME>

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

 
import fileinput
from sets import Set
import random
import scipy.special
import math
import numpy as np
import matplotlib.pyplot as plt
import scipy.stats
from scipy.stats import beta
import pprint, pickle

def VisualizeTopics(phi, words, num_topics, viz_threshold=9e-3):
	phi_viz = np.transpose(phi)
	words_to_display = ~np.all(phi_viz <= viz_threshold, axis=1)
	words_viz = [words[i] for i in range(len(words_to_display)) if words_to_display[i]]
	phi_viz = phi_viz[words_to_display]

	fig, ax = plt.subplots()
	heatmap = plt.pcolor(phi_viz, cmap=plt.cm.Blues, alpha=0.8)
	plt.colorbar()

	#fig.set_size_inches(8, 11)
	ax.grid(False)
	ax.set_frame_on(False)

	ax.set_xticks(np.arange(phi_viz.shape[1]) + 0.5, minor=False)
	ax.set_yticks(np.arange(phi_viz.shape[0]) + 0.5, minor=False)
	ax.invert_yaxis()
	ax.xaxis.tick_top()
	#plt.xticks(rotation=45)
	
	for t in ax.xaxis.get_major_ticks():
	    t.tick1On = False
	    t.tick2On = False
	for t in ax.yaxis.get_major_ticks():
	    t.tick1On = False
	    t.tick2On = False

	column_labels = words_viz	#['Word ' + str(i) for i in range(1,1000)]
	row_labels = ['Topic ' + str(i) for i in range(1,num_topics+1)]
	ax.set_xticklabels(row_labels, minor=False)
	ax.set_yticklabels(column_labels, minor=False)

	plt.show()

def VisualizeEvolution(psi):
	xs = np.linspace(0, 1, num=1000)
	fig, ax = plt.subplots()

	for i in range(len(psi)):
		ys = [math.pow(1-x, psi[i][0]-1) * math.pow(x, psi[i][1]-1) / scipy.special.beta(psi[i][0],psi[i][1]) for x in xs]
		ax.plot(xs, ys, label='Topic ' + str(i+1))

	ax.legend(loc='best', frameon=False)
	plt.show()

def main():
	resultspath = '../results/pnas_tot/'
	tot_pickle_path = resultspath + 'pnas_tot.pickle'

	tot_pickle = open(tot_pickle_path, 'rb')
	par = pickle.load(tot_pickle)
	VisualizeTopics(par['n'], par['word_token'], par['T'])
	VisualizeEvolution(par['psi'])

if __name__ == "__main__":
    main()

# Copyright 2015 <NAME> # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program.  If not, see <http://www.gnu.org/licenses/>. #fig.set_size_inches(8, 11) #plt.xticks(rotation=45) #['Word ' + str(i) for i in range(1,1000)]