# do imports
import matplotlib.pyplot as plt
import numpy as np
import logomaker as logomaker

# load saliency matrix
nn_df = logomaker.get_example_matrix('nn_saliency_matrix',
                                     print_description=False)

# create Logo object
nn_logo = logomaker.Logo(nn_df)

# style using Logo methods
nn_logo.style_spines(visible=False)
nn_logo.style_spines(spines=['left'], visible=True, bounds=[0, .75])

# style using Axes methods
nn_logo.ax.set_xlim([20, 115])
nn_logo.ax.set_xticks([])
nn_logo.ax.set_ylim([-.6, .75])
nn_logo.ax.set_yticks([0, .75])
nn_logo.ax.set_yticklabels(['0', '0.75'])
nn_logo.ax.set_ylabel('                 saliency', labelpad=-1)

# set parameters for drawing gene
exon_start = 55-.5
exon_stop = 90+.5
y = -.2
xs = np.arange(-3, len(nn_df),10)
ys = y*np.ones(len(xs))

# draw gene
nn_logo.ax.axhline(y, color='k', linewidth=1)
nn_logo.ax.plot(xs, ys, marker='4', linewidth=0, markersize=7, color='k')
nn_logo.ax.plot([exon_start, exon_stop],
                [y, y], color='k', linewidth=10, solid_capstyle='butt')

# annotate gene
nn_logo.ax.plot(exon_start, 1.8*y, '^k', markersize=15)
nn_logo.ax.text(20,2*y,'$U2SURP$',fontsize=12)
nn_logo.ax.text(exon_start, 2.5*y,'chr3:142,740,192', verticalalignment='top', horizontalalignment='center')

# show plot
nn_logo.fig.show()