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Added resubmission materials to the webpage
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@gchure
gchure committed Jul 10, 2019
1 parent f3621fb commit 3558160
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Showing 6 changed files with 73 additions and 19 deletions.
13 changes: 11 additions & 2 deletions code/figures/Chure2019_FigS11_DNA_pairwise_comparison.py
View file
Expand Up @@ -58,9 +58,17 @@
else:
face = color[g]
edge = color[g]
if g == 'Y20I':
label = 'Y17I'
elif g == 'Q21A':
label = 'Q18A'
elif g == 'Q21M':
label = 'Q18M'
else:
label = g
_ = ax[i, j].errorbar(_d['IPTGuM'], _d['mean'], _d['sem'], markerfacecolor=face,
markeredgecolor=edge, color=edge, lw=0.15, linestyle='none', fmt='o',
ms=2.5, label=g)
ms=2.5, label=label)

# Plot the best-fit lines.
for k, m in enumerate(data['mutant'].unique()):
Expand All @@ -84,4 +92,5 @@

_ = ax[0, 3].legend(fontsize=8, bbox_to_anchor=(1.04, 0.95))
plt.subplots_adjust(wspace=0.05, hspace=0.05)
plt.savefig('../../figures/Chure2019_FigS11_DNA_pairwise_comparison.pdf', bbox_inches='tight')
plt.savefig('../../figures/Chure2019_FigS12_DNA_pairwise_comparison.pdf',
facecolor='white', bbox_inches='tight')
14 changes: 11 additions & 3 deletions code/figures/Chure2019_FigS12_DNA_deltaF_pairwise_comparisons.py
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Expand Up @@ -37,7 +37,15 @@

# Add titles and row labels.
for m, a in cols.items():
ax[0, a].set_title(m, fontsize=6, y=1.08, backgroundcolor=colors['pale_yellow'])
if m == 'Y20I':
label = 'Y17I'
elif m == 'Q21A':
label = 'Q18A'
elif m == 'Q21M':
label = 'Q18M'
else:
label = m
ax[0, a].set_title(label, fontsize=6, y=1.08, backgroundcolor=colors['pale_yellow'])

for r, a in rows.items():
ax[a, 0].text(-0.3, 0.57, f'R = {int(r)}', fontsize=6, rotation='vertical',
Expand Down Expand Up @@ -93,5 +101,5 @@
epRA['hpd_max'] - constants['O2'], alpha=0.75,
color=rep_colors[r])
plt.subplots_adjust(hspace=0.05, wspace=0.03)
plt.savefig('../../figures/Chure2019_FigS12_DNA_deltaF_pairwise_comparison.pdf',
bbox_inches='tight')
plt.savefig('../../figures/Chure2019_FigS13_DNA_deltaF_pairwise_comparison.pdf',
bbox_inches='tight', facecolor='white')
20 changes: 15 additions & 5 deletions code/figures/Chure2019_FigS17-FigS18_IND_pairwise_comparison.py
View file
Expand Up @@ -63,9 +63,19 @@
else:
face = color[g]
edge = color[g]
if g == 'F164T':
label = 'F161T'
elif g == 'Q294K':
label = 'Q291K'
elif g == 'Q294V':
label = 'Q291V'
elif g == 'Q294R':
label = 'Q291R'
else:
label = g
_ = ax[i, j].errorbar(_d['IPTGuM'], _d['mean'], _d['sem'], markerfacecolor=face,
markeredgecolor=edge, color=edge, lw=0.15, linestyle='none', fmt='o',
ms=2.5, label=g)
ms=2.5, label=label)

# Plot the best-fit lines.
for k, m in enumerate(data['mutant'].unique()):
Expand Down Expand Up @@ -103,9 +113,9 @@
plt.subplots_adjust(wspace=0.05, hspace=0.05)

if MODEL == 'KaKi_only':
plt.savefig('../../figures/Chure2019_FigS17_KaKi_IND_pairwise_predictions.pdf',
bbox_inches='tight')
plt.savefig('../../figures/Chure2019_FigS18_KaKi_IND_pairwise_predictions.pdf',
bbox_inches='tight', facecolor='white')
elif MODEL == 'KaKi_epAI':
plt.savefig('../../figures/Chure2019_FigS18_KaKi_epAI_IND_pairwise_predictions.pdf',
bbox_inches='tight')
plt.savefig('../../figures/Chure2019_FigS19_KaKi_epAI_IND_pairwise_predictions.pdf',
bbox_inches='tight', facecolor='white')

14 changes: 12 additions & 2 deletions code/figures/Chure2019_FigS19_IND_deltaF_comparison.py
View file
Expand Up @@ -42,7 +42,17 @@

# Set titles
for m, a in muts.items():
ax[0, a].set_title(m, fontsize=6, backgroundcolor=pboc['pale_yellow'], y=1.06)
if m == 'F164T':
label = 'F161T'
elif m == 'Q294K':
label = 'Q291K'
elif m == 'Q294V':
label = 'Q291V'
elif m == 'Q294R':
label = 'Q291R'
else:
label = m
ax[0, a].set_title(label, fontsize=6, backgroundcolor=pboc['pale_yellow'], y=1.06)
for o, a in ops.items():
ax[a, 0].text(-0.53, 0.5, o, fontsize=6, rotation='vertical',
backgroundcolor=pboc['pale_yellow'],
Expand Down Expand Up @@ -101,5 +111,5 @@
color=op_colors[g[1]], alpha=0.5)

plt.subplots_adjust(hspace=0.05, wspace=0.05)
plt.savefig('../../figures/Chure2019_FigS19_deltaF_comparison.pdf',
plt.savefig('../../figures/Chure2019_FigS20_deltaF_comparison.pdf',
bbox_inches='tight')
14 changes: 11 additions & 3 deletions code/figures/Chure2019_FigS20_global_DNA_binding_energy_fit.py
View file
Expand Up @@ -43,7 +43,15 @@
# Define the axes.
axes = {'Q21M':0, 'Q21A':1, 'Y20I':2}
for m, a in axes.items():
ax[0, a].set_title(m, fontsize=8, backgroundcolor=colors['pale_yellow'],
if m == 'Q21M':
label = 'Q18M'
elif m == 'Q21A':
label = 'Q18A'
elif m == 'Y20I':
label = 'Y17I'
else:
label = m
ax[0, a].set_title(label, fontsize=8, backgroundcolor=colors['pale_yellow'],
y=1.08)

# ##############################################################################
Expand Down Expand Up @@ -101,5 +109,5 @@
leg = ax[0, 0].legend(title='rep. / cell', fontsize=6)
leg.get_title().set_fontsize(6)
plt.tight_layout()
plt.savefig('../../figures/Chure2019_FigS20_DNA_global_fit.pdf',
bbox_inches='tight')
plt.savefig('../../figures/Chure2019_FigS22_DNA_global_fit.pdf',
bbox_inches='tight', facecolor='white')
17 changes: 13 additions & 4 deletions code/figures/Chure2019_FigS21_global_KaKi_epAI_fits.py
View file
Expand Up @@ -44,7 +44,17 @@
# Define the axes.
axes = {'Q294K':0, 'Q294R':1, 'F164T':2, 'Q294V':3}
for m, a in axes.items():
ax[0, a].set_title(m, fontsize=8, backgroundcolor=colors['pale_yellow'],
if m == 'Q294K':
label = 'Q291K'
elif m == 'Q294R':
label = 'Q291R'
elif m == 'Q294V':
label = 'Q291V'
elif m == 'F164T':
label = 'F161T'
else:
label = m
ax[0, a].set_title(label, fontsize=8, backgroundcolor=colors['pale_yellow'],
y=1.08)

# ##############################################################################
Expand Down Expand Up @@ -107,8 +117,7 @@
leg = ax[0, 0].legend(title='operator', fontsize=6)
leg.get_title().set_fontsize(6)
plt.tight_layout()
plt.savefig('../../figures/Chure2019_FigS21_global_KaKi_epAI_fits.pdf',
bbox_inches='tight')
plt.savefig('../../figures/Chure2019_FigS23_global_KaKi_epAI_fits.pdf',
bbox_inches='tight', facecolor='white')


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