def main():
args = parse_args()
tags = ['staplestates{}'.format(i) for i in range(1, args.stapletypes + 1)]
filebase = '{}/{}-{}'.format(args.input_dir, args.system, args.vari)
out_filebase = '{}/{}-{}_staplestates-means'.format(args.output_dir,
args.system, args.vari)
figsize = (plot.cm_to_inches(18), plot.cm_to_inches(12))
plot.set_default_appearance()
f = plt.figure(figsize=figsize, dpi=300)
gs = gridspec.GridSpec(1, 2, width_ratios=[10, 1], height_ratios=[1])
ax = create_axis(f, gs, args.system)
aves, stds = plot.read_expectations(filebase)
if args.rtag:
aves = aves[aves[args.rtag] == args.rvalue]
stds = stds[stds[args.rtag] == args.rvalue]
for j, tag in enumerate(tags):
xvars = aves[args.xtag]
ax.errorbar(xvars, aves[tag], yerr=stds[tag], marker='o')
# Write to file
plt.tight_layout(pad=0.5, h_pad=0, w_pad=0)
f.savefig(out_filebase + '.png', transparent=True)
f.savefig(out_filebase + '.pdf', transparent=True)
def main():
args = parse_args()
inp_filebase = '{}/{}-{}'.format(args.input_dir, args.system, args.vari)
out_filebase = '{}/{}-{}_staplestates-melting'.format(args.output_dir,
args.system, args.vari)
index_to_stapletype = np.loadtxt(args.mapfile, dtype=int)
figsize = (plot.cm_to_inches(18), plot.cm_to_inches(12))
plot.set_default_appearance()
f = plt.figure(figsize=figsize, dpi=300)
gs = gridspec.GridSpec(1, 1, width_ratios=[1], height_ratios=[1])
gs_main = gridspec.GridSpecFromSubplotSpec(1, 1, subplot_spec=gs[:, :])
ax = f.add_subplot(gs_main[0])
ax.axis('off')
aves, stds = plot.read_expectations(inp_filebase)
if args.rtag:
aves = aves[aves[args.rtag] == args.rvalue]
stds = stds[stds[args.rtag] == args.rvalue]
temps = aves.temp
melting_points = estimate_melting_points(args.stapletypes, aves, temps)
melting_array = fill_assembled_shape_array(melting_points, index_to_stapletype)
# Plot simulation melting points
min_t = np.min(melting_array)
max_t = np.max(melting_array)
im = ax.imshow(melting_array, vmin=min_t, vmax=max_t)
plt.colorbar(im, orientation='horizontal')
plt.tight_layout(pad=0.5, h_pad=0, w_pad=0)
f.savefig(out_filebase + '.png', transparent=True)
f.savefig(out_filebase + '.pdf', transparent=True)
def main():
args = parse_args()
tags = ['numstaples', 'numfulldomains', 'nummisdomains', 'numstackedpairs']
yaxis_labels = [
'(Mis)bound staples', 'Bound domain pairs', 'Misbound domain pairs',
'Stacked pairs'
]
figsize = (plot.cm_to_inches(14), plot.cm_to_inches(11))
plot.set_default_appearance()
f = plt.figure(figsize=figsize, dpi=300)
gs = gridspec.GridSpec(3,
2,
width_ratios=[1, 1],
height_ratios=[10, 10, 1])
gs_main = gridspec.GridSpecFromSubplotSpec(2,
2,
subplot_spec=gs[:2, :],
wspace=0.3,
hspace=0.3)
axes = create_axes(f, gs_main, yaxis_labels)
all_assembled_values = []
for assembled_values in args.all_assembled_values:
parsed_values = []
for assembled_value in assembled_values.split(','):
parsed_values.append(int(assembled_value))
all_assembled_values.append(parsed_values)
for assembled_values in all_assembled_values:
for i, assembled_value in enumerate(assembled_values):
ax = axes[i]
ax.axhline(assembled_value, linestyle='--', color='0.8')
for system, vari in zip(args.systems, args.varis):
sim_filebases = '{}/{}-{}'.format(args.input_dir, system, vari)
all_aves, all_stds = plot.read_expectations(sim_filebases)
xvars = all_aves[args.xtag]
for i, tag in enumerate(tags):
means = all_aves[tag]
stds = all_stds[tag]
ax = axes[i]
ax.errorbar(xvars, means, yerr=stds, marker='o', label=vari)
# Plot legend
gs_lgd = gridspec.GridSpecFromSubplotSpec(1, 1, subplot_spec=gs[2, :])
ax = f.add_subplot(gs_lgd[0])
ax.set_axis_off()
handles, labels = axes[0].get_legend_handles_labels()
ax.legend(handles, labels, loc='center', frameon=False, ncol=1)
gs.tight_layout(f, pad=1.0, h_pad=0, w_pad=0)
f.savefig(args.output_filebase + '.png', transparent=True)
f.savefig(args.output_filebase + '.pdf', transparent=True)
def main():
args = parse_args()
op_tag = 'numfulldomains'
tagbase = 'domainstate'
tags = ['{}{}'.format(tagbase, i) for i in range(args.scaffolddomains)]
inp_filebase = '{}/{}-{}-{}'.format(args.input_dir, args.system, args.vari,
op_tag)
index_to_domaintype = np.loadtxt(args.mapfile, dtype=int)
figsize = (plot.cm_to_inches(18), plot.cm_to_inches(12))
for op_value in range(1, args.scaffolddomains + 1):
out_filebase = '{}/{}-{}_{}-{}-{}-freqs'.format(
args.output_dir, args.system, args.vari, op_tag, op_value, tagbase)
plot.set_default_appearance()
f = plt.figure(figsize=figsize, dpi=300)
gs = gridspec.GridSpec(1, 1, width_ratios=[1], height_ratios=[1])
gs_main = gridspec.GridSpecFromSubplotSpec(1, 1, subplot_spec=gs[:, :])
ax = f.add_subplot(gs_main[0])
ax.axis('off')
aves, stds = plot.read_expectations(inp_filebase)
if not op_value in aves[op_tag].values:
continue
reduced_aves = aves[aves[op_tag] == op_value]
freqs = [reduced_aves[t] for t in tags]
freq_array = fill_assembled_shape_array(freqs, index_to_domaintype)
# Plot simulation melting points
min_t = np.min(0)
max_t = np.max(1)
im = ax.imshow(freq_array, vmin=min_t, vmax=max_t)
plt.colorbar(im, orientation='horizontal')
plt.tight_layout(pad=0.5, h_pad=0, w_pad=0)
f.savefig(out_filebase + '.png', transparent=True)
f.savefig(out_filebase + '.pdf', transparent=True)
def main():
args = parse_args()
tags = ['numstaples', 'numfulldomains', 'nummisdomains', 'numstackedpairs']
yaxis_labels = [
'(Mis)bound staples', 'Bound domain pairs', 'Misbound domain pairs',
'Stacked pairs'
]
figsize = (plot.cm_to_inches(14), plot.cm_to_inches(11))
plot.set_default_appearance()
f = plt.figure(figsize=figsize, dpi=300)
gs = gridspec.GridSpec(3,
2,
width_ratios=[1, 1],
height_ratios=[10, 10, 1])
gs_main = gridspec.GridSpecFromSubplotSpec(2,
2,
subplot_spec=gs[:2, :],
wspace=0.3,
hspace=0.3)
gs_cb = gridspec.GridSpecFromSubplotSpec(1, 1, subplot_spec=gs[2, :])
axes = create_axes(f, gs_main, yaxis_labels)
norm = mpl.colors.Normalize(vmin=args.smults[0], vmax=args.smults[-1])
cmap = mpl.cm.viridis
scalarmap = mpl.cm.ScalarMappable(norm=norm, cmap=cmap)
all_assembled_values = []
for assembled_values in args.all_assembled_values:
parsed_values = []
for assembled_value in assembled_values.split(','):
parsed_values.append(int(assembled_value))
all_assembled_values.append(parsed_values)
for assembled_values in all_assembled_values:
for i, assembled_value in enumerate(assembled_values):
ax = axes[i]
ax.axhline(assembled_value, linestyle='--', color='0.8')
for system, vari in zip(args.systems, args.varis):
sim_filebases = '{}/{}-{}'.format(args.input_dir, system, vari)
all_aves, all_stds = plot.read_expectations(sim_filebases)
for smult in args.smults:
reduced_aves = all_aves[all_aves['bias'] == smult]
reduced_stds = all_stds[all_stds['bias'] == smult]
xvars = reduced_aves['temp']
for i, tag in enumerate(tags):
means = reduced_aves[tag]
stds = reduced_stds[tag]
ax = axes[i]
ax.errorbar(xvars,
means,
yerr=stds,
marker='o',
label=vari,
color=scalarmap.to_rgba(smult))
# Plot legend
ax = f.add_subplot(gs_cb[0])
cbar = mpl.colorbar.ColorbarBase(ax,
orientation='horizontal',
cmap=cmap,
norm=norm)
gs.tight_layout(f, pad=1.0, h_pad=0, w_pad=0)
f.savefig(args.output_filebase + '.png', transparent=True)
f.savefig(args.output_filebase + '.pdf', transparent=True)