def mut_counts(cons, seqs, name = promoter_type):
l = len(cons)
figtitle = '{0}_mut_counts'.format(name)
f = myplots.fignum(1, (8,8))
ax = f.add_subplot(111)
counts = zeros(( 4, l))
lets = ['A','T','G', 'C']
for pos in range(l):
counts[:,pos] = [0 if let == cons[pos] else list(seqs[:,pos]).count(let)
for let in lets ]
seismic.seismic(counts, ax = ax)
f.savefig(figtemplate.format(figtitle))
def plot_ronn(**kwargs):
l5 = last_5(**mem.sr(kwargs))
ys = zeros((len(l5), len(l5.values()[0])))
for i, h in enumerate(l5.values()):
for j, d in enumerate(h):
if len(d) == 0:
continue
cas = [e.created_at for e in d]
secs = np.sum([(((ca.hour) * 60 + ca.minute) * 60) + ca.second for ca in cas])
ys[i, j] = secs
ys = ys[:, -20:]
ys = ys - np.min(ys, 1)[:, newaxis]
colors = mycolors.getct(len(ys))
seismic.seismic(ys, stacked=True, colors=colors)
def show_errors(errors, staysames, improves, gnames):
figtitle = "show_errors"
f = myplots.fignum(3, (12, 6))
ax = f.add_axes([0.05, 0.05, 0.25, 0.9])
import scipy.signal as ss
for all_errs in errors[0:1]:
for e in all_errs.flatten()[:5]:
ax.plot(ss.medfilt(e.flatten() ** 2, 51))
get_worse = 1 - (array(staysames) + array(improves))
ax2 = f.add_axes([0.3, 0.05, 0.65, 0.9])
seismic.seismic(
squeeze([get_worse, staysames, improves]),
stacked=True,
colors=[[1, 0, 0], [0, 0, 0], [0, 0, 1]],
ax=ax2,
linewidth=10,
label_y=False,
)
f.savefig(figtemplate.format(figtitle))
colors = random.rand(len(top), 3)
if do_seismic:
try:
import cb.utils.seismic as seismic
print 'no problem'
do_seismic = True
except Exception, e:
print 'problem (seismic is unavailable)?'
if do_seismic:
f2 = plt.figure(2)
ax2 = f2.add_subplot(111)
seismic.seismic(yvals,
colors=colors,
labels=top_keys,
stacked=False,
ax=ax2)
else:
f2 = plt.figure(2)
ax2 = f2.add_subplot(111)
for i, ys in enumerate(yvals):
ax2.plot(range(24), ys, color=colors[i], label=top_keys[i])
ax2.plot(mean(yvals, 0),
linewidth=5,
color='black',
label='mean for top subids')
ax2.set_xlabel('hour')
ax2.set_ylabel(hour_key)
print '{0} is the best hour (military time)'\
if do_seismic:
try:
import cb.utils.seismic as seismic
print 'no problem'
do_seismic = True
except Exception, e:
print 'problem (seismic is unavailable)?'
if do_seismic:
f2 = plt.figure(2)
ax2 = f2.add_subplot(111)
seismic.seismic(yvals, colors = colors,
labels = top_keys,
stacked = False,
ax = ax2)
else:
f2 = plt.figure(2)
ax2 = f2.add_subplot(111)
for i, ys in enumerate(yvals):
ax2.plot(range(24), ys, color = colors[i],
label = top_keys[i])
ax2.plot(mean(yvals,0),linewidth = 5, color = 'black',
label = 'mean for top subids')
ax2.set_xlabel('hour')
ax2.set_ylabel(hour_key)
print '{0} is the best hour (military time)'\
.format(argmax(mean(yvals,0)))
ax2.legend()
