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()