Analysis of Groove Widths in Periodic DNA

In [1]:

    

%matplotlib inline
import matplotlib.pyplot as plt
from pylab import rcParams
# a couple changes to make the matplotlib figures bigger
rcParams['figure.figsize'] = 12, 8
rcParams['font.size'] = 20

import numpy as np
import pyna


    

In [2]:

    

periodic = pyna.CurvesAnalysis('../curves_output.data')


    

In [3]:

    

minor = pyna.StrandStatistics(periodic.panels['groupE']['w12'])
major = pyna.StrandStatistics(periodic.panels['groupE']['w21'])


    

In [4]:

    

minor_means = minor.mean(per_location=True)
major_means = major.mean(per_location=True)
minor_stds = minor.std(per_location=True)
major_stds = major.std(per_location=True)
xvals = minor.df.columns.values


    

In [5]:

    

plt.figure()
plt.errorbar(xvals, minor_means, yerr=minor_stds)
plt.errorbar(xvals, major_means, yerr=major_stds)
plt.xlabel("Base pair number")
plt.ylabel("Groove width")
plt.gca().set_ylim(ymin=0); # force the yaxis to go to 0


    

    
Out[5]:





(0, 16.0)






    

In [6]:

    

pyna.AnimatedDataFrame(minor.df).show()


    

    
Out[6]:

In [7]:

    

minor_hist = minor.hist(per_location=True, bins=28, range=(0.0, 14.0))


    

In [8]:

    

plt.pcolor(minor_hist)
plt.yticks(np.arange(0.5, len(minor_hist.index), 2), minor_hist.index[::2])
plt.xticks(np.arange(0.5, len(minor_hist.columns), 5), minor_hist.columns[::5])
plt.xlabel("Base pair number")
plt.ylabel("Minor groove width")
plt.show()


    

In [9]:

    

plt.plot(minor_hist.index, minor_hist[19.0])
plt.plot(minor_hist.index, minor_hist[20.5])


    

    
Out[9]:





[<matplotlib.lines.Line2D at 0x11221d990>]






    

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