all_distance_plots.py

# these lines needed for working on ELF -- feel free to comment out
import sys
sys.path.append("/usr/lib64/python2.7/site-packages")
sys.path.append("/usr/lib/python2.7/site-packages/decorator-3.4.0-py2.7.egg")
sys.path.append("/usr/lib/python2.7/site-packages")

import plotting
import argparse
from matplotlib import pyplot as plt
import os

plt.rc('axes.formatter', use_mathtext=True)

parser = argparse.ArgumentParser()

# path to folder containing ppi and GO files
# organisms is a string of organisms we want to generate plots for, separated by spaces
parser.add_argument("directory")
parser.add_argument("organisms")

# # file to write LaTeX code to
# parser.add_argument("outfile")

options = parser.parse_args()

organisms = options.organisms.split(' ')

# ppi file extension
ppiExt = ".ppi"

# folder we want to put plots in
plotsDir = "plots"

# assume that any npy matrices will be in this folder
# if folder doesnt exist, create
npyDir = "NumPy files"
try:
    os.makedirs(npyDir)
except OSError:
    if not os.path.isdir(npyDir):
        raise

distanceMetrics = {}

figNum = 1
for organism in organisms:
    # setup
    print("generating plots for: " + organism)
    infile = options.directory + "/" + organism + ppiExt

    # distanceMetrics['DSD 50LM'] = npyDir + "/dsd_50/" + organism + "_dsd.npy"
    # distanceMetrics['DSD 50LM (random)'] = npyDir + "/dsd_50_random/" + organism + "_dsd.npy"
    # distanceMetrics['DSD 200LM'] = npyDir + "/dsd_200/" + organism + "_dsd.npy"
    # distanceMetrics['DSD 200LM (random)'] = npyDir + "/dsd_200_random/" + organism + "_dsd.npy"
    # distanceMetrics['DSD 500LM'] = npyDir + "/dsd_500/" + organism + "_dsd.npy"
    # distanceMetrics['DSD 500LM (random)'] = npyDir + "/dsd_500_random/" + organism + "_dsd.npy"
    # distanceMetrics['SPD'] = npyDir + "/" + organism + "_spd.npy"

    # pyplot uses 7 built-in colors, so easier to stick to plotting 7 at a time.
    distanceMetrics['DFD'] = npyDir + "/" + organism + "_dfd.npy"
    distanceMetrics['DSD 500LM'] = npyDir + "/dsd_500/" + organism + "_dsd.npy"
    distanceMetrics['DSD 500LM (random)'] = npyDir + "/dsd_500_random/" + organism + "_dsd.npy"
    distanceMetrics['DSD 500LM (eigen)'] = npyDir + "/dsd_500_eigen/" + organism + "_dsd.npy"
    distanceMetrics['DSD 500LM (katz)'] = npyDir + "/dsd_500_katz/" + organism + "_dsd.npy"
    distanceMetrics['DSD 500LM (closeness)'] = npyDir + "/dsd_500_closeness/" + organism + "_dsd.npy"
    distanceMetrics['DSD 500LM (betweenness)'] = npyDir + "/dsd_500_betweenness/" + organism + "_dsd.npy"

    plt.figure(figNum)
    plotting.all_distance_pairs_density(infile, distanceMetrics=distanceMetrics, \
        overlapMat=npyDir + "/" + organism + "_overlap.npy")

    # save plot
    figFile = plotsDir + "/" + organism + "_alld_pairs_density"
    figFile += ".png"
    plt.savefig(figFile)
    figNum += 1