fig.add_subplot(ax1)
ax2 = ax1.twin()
ax1.imshow(emat,interpolation='nearest')
ax1.set_xlabel('Position w.r.t. transcription start site')
ax1.set_yticks([0,1,2,3])
ax1.set_yticklabels(['A','C','G','T'])
# label positions with respect to transcription start site
tick_start = int(start_dict[info_dict['exp_name']])+int(info_dict['mut_region_start'])
tick_end = int(start_dict[info_dict['exp_name']])+int(info_dict['mut_region_start']) + int(info_dict['mut_region_length'])
indices, xtick_labels = clean_up_xticklabels(tick_start,tick_end-tick_start)
ax1.set_xticks(indices)
ax1.set_xticklabels(xtick_labels)
# put the sequence above it
ax2.set_yticks([])
ax2.set_yticklabels([])
ax2.set_xticks(range(20))
ax2.set_xticklabels([bp for bp in site_seq])
#plt.title('$lac$ promoter, -35 region')
if 'conditional' in infofn[namedict[fn]]:
condbase = str(int(start_dict[info_dict['exp_name']]) + int(info_dict['condbase']))
plt.text(0.5,1.25,'Conditional Matrix: ' + info_dict['condident'] + ' at ' + condbase, horizontalalignment='center', fontsize=12, transform = ax2.transAxes)
else:
plt.text(0.5,1.25,'Energy Matrix: ' + str(tick_start) + ' to ' + str(tick_end),horizontalalignment='center', fontsize=12, transform = ax2.transAxes)
plt.show()
plt.savefig(os.path.join(outputdir,fnname + 'emat' + str(tick_start) + ' to ' + str(tick_end) + '.pdf'))
ax2 = ax1.twin()
ax1.imshow(emat, interpolation='nearest')
ax1.set_xlabel('Position w.r.t. transcription start site')
ax1.set_yticks([0, 1, 2, 3])
ax1.set_yticklabels(['A', 'C', 'G', 'T'])
# label positions with respect to transcription start site
tick_start = int(start_dict[info_dict['exp_name']]) + int(
info_dict['mut_region_start'])
tick_end = int(start_dict[info_dict['exp_name']]) + int(
info_dict['mut_region_start']) + int(
info_dict['mut_region_length'])
indices, xtick_labels = clean_up_xticklabels(tick_start,
tick_end - tick_start)
ax1.set_xticks(indices)
ax1.set_xticklabels(xtick_labels)
# put the sequence above it
ax2.set_yticks([])
ax2.set_yticklabels([])
ax2.set_xticks(range(20))
ax2.set_xticklabels([bp for bp in site_seq])
#plt.title('$lac$ promoter, -35 region')
if 'conditional' in infofn[namedict[fn]]:
condbase = str(
int(start_dict[info_dict['exp_name']]) +
int(info_dict['condbase']))
plt.text(0.5,
1.25,
'Conditional Matrix: ' + info_dict['condident'] + ' at ' +
for n in range(1, 4, 1):
ax_wn = SubplotHost(fig, 1, 3, n)
fig.add_subplot(ax_wn)
ax_wn.set_xlim(700, 1700)
x_wn = np.array([800, 1000, 1200, 1400, 1600])
ax_wn.tick_params(axis='x',
direction='in',
labelsize=11,
labelbottom=False,
labeltop=True,
top=True,
bottom=False)
ax_wn.tick_params(axis='y', left=False, labelleft=False)
ax_wn.set_xticks(x_wn)
ax_mn = ax_wn.twin(aux_trans)
ax_mn.set_viewlim_mode("transform")
# x_micron=np.array([12, 10, 8, 6])
# ax_mn.set_xticks(x_micron)
ax_mn.tick_params(axis='x',
direction='in',
labelsize=11,
labelbottom=True,
labeltop=False,
top=False,
bottom=True)
ax_mn.tick_params(axis='y', right=False, labelright=False)
