58_silent_to_nonsilent_plot.py

#!/usr/bin/python3 -u
#
# This source code is part of icgc, an ICGC processing pipeline.
# 
# Icgc 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.
# 
# Icgc 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/>.
# 
# Contact: ivana.mihalek@gmail.com
#

import matplotlib.pyplot as plt


#########################################
def main():

	# extras = ['RPL5', 'RPL11', 'RPL22',
	#           'TP53','TTN', 'PTEN', 'SMAD4','SETD2',
	#           'RB1', 'VHL', 'PIK3CA', 'IDH1',
	#           'WDR41',
	#           'RABAC1','BEX5', 'DEFB116', 'NODAL','DDX3X','RAD9B', 'LUC7L2', 'FZD10',
	#            'ATM' ,  'BRCA2', 'NF1', 'CASP8', 'TSGA10',
	#           'BBX','B2M',
	#           'SOS1','FBXW7','GNAS',
	#           'PIK3CA', 'ZC3H13', 'APC',
	#           'BRCA1','MTOR', 'KRAS' , 'MDM2',
	#           'TBL1XR1', 'UBC', 'HSPA1L', 'SP8',
	#           'VHL', 'BRAF', 'MUC2', 'MUC4', 'NPM1']

	zoom  = True
	label = False # a bug in matplot lib: x-axis labels cannot be turned off for zoom

	if zoom:
		extras = ['RPL5', 'RPL11', 'RPL22',
		          'TP53','TTN', 'PTEN', 'SMAD4','SETD2',
		          'RB1', 'VHL',
		          'WDR41',
		          'RABAC1','BEX5', 'DEFB116', 'RAD9B', 'LUC7L2', 'FZD10',
		          'NPM1' ,  'BRCA2',  'CASP8',  'B2M',
		          'SOS1',
		          'PIK3CA', 'APC',
		          'BRCA1','MTOR', 'KRAS' , 'MDM2',
		          'UBC', 'HSPA1L', 'SP8',
		          'VHL', 'BRAF', 'MUC2', 'MUC4']
	else:
		extras = ['BEX5','PTEN','TP53','TTN', 'HSPA1L','MUC16']


	inf = open("silent_ratio.tsv","r")
	x = []
	y = []
	coords = {}
	for line in inf:
		[gene, ratio, totct] = line.split('\t')
		ratio = float(ratio)
		totct = int(totct)
		x.append(ratio)
		y.append(totct)
		for extra in extras:
			if gene == extra: coords[extra] = [ratio,totct]


	# s is marker size in points**2
	plt.xscale('log')
	plt.yscale('log')

	if zoom:
		plt.xlim(0.06,0.3)
		plt.ylim(50,1000)
		plt.scatter(x,y,s=0.5, c='#17aad3')
		if label:
			plt.xlabel('SILENT MUTATION FRACTION', fontsize=16)
			plt.ylabel('TOTAL NUMBER OF MUTATIONS', fontsize=16)
			label_offset_x = 0.003
			label_offset_y = 5
			fontsize=12

	else: # full pic
		plt.xlim(0.025,1)
		plt.ylim(10,11000)
		plt.scatter(x,y,s=1,c='#17aad3')
		if label:
			label_offset_x = 0.0
			label_offset_y = 0
			fontsize=15

	# hiding the axis labels
	if not label:
		frame = plt.gca()
		frame.tick_params(labelbottom='off')
		frame.tick_params(labelleft='off')

	for extra in extras:
		plt.plot(coords[extra][0], coords[extra][1],'ro',mfc='none')
		if label:
			annotcoords = [coords[extra][0] + label_offset_x, coords[extra][1]+label_offset_y]
			plt.annotate(extra, annotcoords, color="r", fontsize=fontsize)#, fontweight='bold')


	if zoom: plt.savefig("zoom.svg", format="svg")
	plt.show()

#########################################
if __name__ == '__main__':
	main()


'''
% HSPA1L
% 
https://www.nature.com/articles/onc2017263?WT.feed_name=subjects_cancer

% BEX5 > poorly described, brain expressed
% PTEN well-stuided tumor suppressor 
#https://www.annualreviews.org/doi/abs/10.1146/annurev.pathol.4.110807.092311

'''