scatterplot

import matplotlib.pyplot as plt
import matplotlib.patches as mplpatches
import numpy as np
import time
import scipy.stats as stats
import argparse

parser=argparse.ArgumentParser()
parser.add_argument('-i','--input_file')
parser.add_argument('-s','--style_sheet',default='BME163')
args=parser.parse_args()
inputFile=args.input_file
styleSheet=args.style_sheet
plt.style.use(styleSheet)

mainpanelWidth=1.5
mainpanelHeight=2
figureWidth=3
figureHeight=3

relativeMainPanelWidth=mainpanelWidth/figureWidth
relativeMainPanelHeight=mainpanelHeight/figureHeight

mainPanel=plt.axes([0.1,0.2,relativeMainPanelWidth,relativeMainPanelHeight])

blue=(0,0,1)
red=(1,0,0)
green=(0,1,0)
yellow=(1,1,0)
black=(0,0,0)
white=(1,1,1)

for a in open(inputFile):
    line= a.strip().split('\t')
    if line[1] != 'NA' and line[2] != 'NA':
        fold_change = float(line[1])
        pvalue = -(np.log10(float(line[2])))
        ID = line[0]
        if 2**abs(fold_change) > 10 and pvalue > 8:
            mainPanel.scatter(fold_change, pvalue,s=4, c=(1,0,0), 
            linewidth=0)
        else:
            mainPanel.scatter(fold_change, pvalue, s=4, c=(0,0,0),
            linewidth=0)
        if 2**-(fold_change) > 10 and pvalue > 30:
            mainPanel.text(fold_change, pvalue, ID, horizontalalignment='right',fontsize=8)

mainPanel.set_xlim(-12,12)
mainPanel.set_ylim(0,60)
mainPanel.set_xlabel('log$_{2}$(fold change)')
mainPanel.set_ylabel('-log$_{10}$(p-value)')

mainPanel.set_yticks([0,20,40,60])

        
plt.savefig('Assignment3.pdf',dpi=600)