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updated figures for preprint
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Chaitanya CHINTALURI committed Oct 7, 2022
1 parent d6c2d9e commit 368918e
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Showing 5 changed files with 254 additions and 119 deletions.
84 changes: 52 additions & 32 deletions fig1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ def quantum(ax1):
Qval = np.zeros_like(tt)
vals = Q_nak(tt, 30)
Qval[int(150/dt):] += vals[:len(Qval[int(150/dt):])]

lns = ax1.plot(tt, Qval, color='w', alpha=0) # fake line
points = np.array([tt, Qval]).T.reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
norm = plt.Normalize(0, 500)
Expand All @@ -87,8 +87,10 @@ def quantum(ax1):
empty_string_labels = [' ']*len(labels)
ax1.set_yticklabels(empty_string_labels)
ax1.plot(-25, 0, marker='*', c='k', clip_on=False, markersize=7.5,
markeredgecolor='none')
markeredgewidth=0.5, markeredgecolor='white', zorder=10)
ax1.text(s='+Q', x=85, y=27.5, fontsize=7)
fp.add_arrow(lns[0], position=155, color='k', size=6.5)
fp.add_arrow(lns[0], position=300, color='k', size=6.5)
ax1.set_xlim(-25, 500)


Expand Down Expand Up @@ -137,8 +139,10 @@ def excursion(ax2):
ax2.set_ylim(0, 1.)
ax2.set_xticks([0, 0.5, 1])
ax2.set_yticks([0, 0.5, 1])
ax2.set_xticklabels([0, '', 1])
ax2.set_yticklabels([0, '', 1])
ax2.set_xlabel('$ATP_M$')
ax2.set_ylabel(r'$\Delta\psi$')
ax2.set_ylabel(r'$\Delta\psi$', rotation=0)
return ax2


Expand Down Expand Up @@ -190,9 +194,9 @@ def ros_land(ax, cax=None):
boxstyle=bstyle,
alpha=0.5, zorder=10, facecolor='None',
edgecolor='#d01c8b', linewidth=2)
ax.text(0.07, -.1, 'FETROS',
ax.text(0.07, .5, 'FETROS',
fontsize=7, color='#d01c8b').set_clip_on(False)
ax.text(0.65, 0.45, 'RETROS',
ax.text(0.65, 1.05, 'RETROS',
fontsize=7, color='#4dac26').set_clip_on(False)
retbox.set_clip_on(False)
fetbox.set_clip_on(False)
Expand All @@ -203,8 +207,10 @@ def ros_land(ax, cax=None):
ax.set_ylim(0, 1)
ax.set_xticks([0, 0.5, 1])
ax.set_yticks([0, 0.5, 1])
ax.set_xticklabels([0, '', 1])
ax.set_yticklabels([0, '', 1])
ax.set_xlabel(r'$ATP_M$')
ax.set_ylabel(r'$\Delta\psi$')
ax.set_ylabel(r'$\Delta\psi$', rotation=0)
return ax, surf


Expand Down Expand Up @@ -318,35 +324,44 @@ def figure_steady_state_simpler(ax1):

kANT_units = '10$^{-3}$/s'
# half a column size is
figsize = fp.cm_to_inches([8.9, 13.])
figsize = fp.cm_to_inches([8.9, 13.5])
fig = plt.figure(figsize=figsize)
fig.set_constrained_layout_pads(w_pad=0, h_pad=0)
gs = gridspec.GridSpec(3, 2, figure=fig, height_ratios=[1.35, 1.35, 1],
width_ratios=[1, 1])

gs22 = gridspec.GridSpecFromSubplotSpec(2, 1, subplot_spec=gs[1, 0],
hspace=0.1)

ax_steadys = fig.add_subplot(gs[0, 0])
ax_steadys = figure_steady_state_simpler(ax_steadys)
ax_steadys = fp.add_logticks(ax_steadys)

ax_rosland = fig.add_subplot(gs[0, 1])
ax_rosland = fig.add_subplot(gs[0, 0])
ax_rosland, surf = ros_land(ax_rosland, None)
ax_rosland = plot_bl_curve(ax_rosland)

ax_rosss = fig.add_subplot(gs[2, 0])
ax_rosss = fig.add_subplot(gs[0, 1])
ax_rosss = ros_ss(ax_rosss)
ax_rosss.spines['top'].set_visible(False)
ax_rosss.spines['right'].set_visible(False)
ax_rosss = fp.add_logticks(ax_rosss)
ax_rosss.tick_params(axis='x', which='major', pad=3)

ax_excursion = fig.add_subplot(gs[1, 0])
excursion(ax_excursion)

gs22 = gridspec.GridSpecFromSubplotSpec(2, 1, subplot_spec=gs[1, 1],
hspace=0.1)
ax_spikecost = fig.add_subplot(gs22[1, 0])
ax_fakespike = fig.add_subplot(gs22[0, 0], sharex=ax_spikecost)
ax_excursion = fig.add_subplot(gs[1, 1])
single_spike(ax_fakespike)
quantum(ax_spikecost)
excursion(ax_excursion)

ax_steadys = fig.add_subplot(gs[2, 0])
ax_steadys = figure_steady_state_simpler(ax_steadys)
ax_steadys = fp.add_logticks(ax_steadys)
ax_steadys.tick_params(axis='x', which='major', pad=3)

ax_compensate = fig.add_subplot(gs[2, 1])
ax_compensate = metabolic_spikes(ax_compensate)
ax_compensate.spines['top'].set_visible(False)
ax_compensate.spines['right'].set_visible(False)
ax_compensate = fp.add_logticks(ax_compensate)
ax_compensate.tick_params(axis='x', which='major', pad=3)

ax_fakespike.spines['top'].set_visible(False)
ax_fakespike.spines['right'].set_visible(False)
Expand All @@ -355,31 +370,36 @@ def figure_steady_state_simpler(ax1):
ax_spikecost.spines['top'].set_visible(False)
ax_spikecost.spines['right'].set_visible(False)

ax_compensate = fig.add_subplot(gs[2, 1])
ax_compensate = metabolic_spikes(ax_compensate)
ax_compensate.spines['top'].set_visible(False)
ax_compensate.spines['right'].set_visible(False)
ax_compensate = fp.add_logticks(ax_compensate)

fp.align_axis_labels([ax_steadys, ax_fakespike,
ax_rosss],
axis='y', value=-0.15)
fp.align_axis_labels([ax_spikecost], axis='y', value=-0.02)
# ax_rosland, ax_rosss
# ax_excursion, ax_fakespike
# ax_excursion, ax_spikecost
# ax_steadys, ax_compensate

fp.align_axis_labels([ax_rosland, ax_excursion,
fp.align_axis_labels([ax_steadys, ax_excursion,
ax_rosland],
axis='y', value=-0.15)
fp.align_axis_labels([ax_rosss, ax_fakespike,
ax_compensate],
axis='y', value=-0.15)
fp.align_axis_labels([ax_steadys],
axis='x', value=-0.14)
fp.align_axis_labels([ax_spikecost], axis='y', value=-0.02)

# fp.align_axis_labels([ax_rosland, ax_excursion,
# ax_compensate],
# axis='y', value=-0.15)

# fp.align_axis_labels([ax_steadys, ax_compensate],
# axis='x', value=-0.2)

fp.align_axis_labels([ax_rosland],
axis='x', value=-0.14)
axis='x', value=-0.1)
fp.align_axis_labels([ax_spikecost],
axis='x', value=-0.28)
fp.align_axis_labels([ax_excursion],
axis='x', value=-0.14)

gs.tight_layout(fig)
rect = 0.6, 0.65, 0.35, 0.01
rect = 0.125, 0.67, 0.33, 0.01
cbaxes = fig.add_axes(rect)
cb = plt.colorbar(surf, cax=cbaxes,
orientation='horizontal', ticks=[0, 1])
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