def plot_fluxes(
flux_dict,
escher_map,
output_file='map.html',
height=600,
width=800,
reaction_scale=None,
min_flux=-10,
max_flux=10,
):
if min_flux is None:
min_flux = min(flux_dict)
if max_flux is None:
max_flux = max(flux_dict)
if reaction_scale is None:
reaction_scale = [{
'type': 'value',
'value': min_flux,
'color': 'red',
'size': 32
}, {
'type': 'value',
'value': 0,
'color': '#c8c8c8',
'size': 12
}, {
'type': 'value',
'value': max_flux,
'color': 'green',
'size': 32
}]
builder = Builder(height=height,
width=width,
map_json=escher_map,
reaction_scale=reaction_scale)
builder.reaction_data = flux_dict
builder.save_html(output_file)
builder.close()
def animate_fluxes(
flux_time_data,
escher_map,
outputfile='animation.mp4',
height=600,
width=800,
time_interval_ms=100,
chrome=DEFAULT_CHROME,
reaction_scale=None,
min_flux=None,
max_flux=None,
time_size=12,
time_unit='h',
x_time=0.95,
y_time=0.9,
):
if min_flux is None:
min_flux = flux_time_data.min().min()
if max_flux is None:
max_flux = flux_time_data.max().max()
if reaction_scale is None:
reaction_scale = [{
'type': 'value',
'value': min_flux,
'color': 'red',
'size': 32
}, {
'type': 'value',
'value': 0,
'color': '#c8c8c8',
'size': 12
}, {
'type': 'value',
'value': max_flux,
'color': 'green',
'size': 32
}]
builder = Builder(height=height,
width=width,
map_json=escher_map,
embedd_css=EMBEDD_CSS,
menu='none',
reaction_scale=reaction_scale)
myimages = []
fig = plt.figure()
XVFB_DOCKER = '/usr/bin/xvfb-run -a -s \"-screen 0 {}x{}x24\"'.format(
width, height)
SCREENSHOT = "--headless --disable-gpu --no-sandbox --virtual-time-budget=10000 --screenshot=\'{}\' {}"
for t, fluxes in flux_time_data.iterrows():
builder.reaction_data = fluxes
builder.save_html('tmp.html', )
# Hacky hack hack ...
# Use chrome to make a screenshot
cmd = "{} {} {}".format(XVFB_DOCKER, chrome,
SCREENSHOT.format('tmp.png', 'tmp.html'))
os.system(cmd)
# Add time text
ylim = plt.gca().get_ylim()
xlim = plt.gca().get_xlim()
y = (ylim[1] - ylim[0]) * y_time + ylim[0]
x = (xlim[1] - xlim[0]) * x_time + xlim[0]
text = plt.text(x,
y,
'{:.1f} {}'.format(t, time_unit),
horizontalalignment='right',
fontsize=time_size)
img = mgimg.imread('tmp.png')
imgplot = plt.imshow(img)
# append AxesImage object to the list
myimages.append([imgplot, text])
plt.axis('off')
fig.tight_layout()
anim = animation.ArtistAnimation(fig, myimages, interval=time_interval_ms)
anim.save(outputfile, dpi=300)
builder.close()
