def plot(cfg, name, fig, canvas, ax, entities, xlabel=' ', ylabel=None, yticks=None):
quodplot = quod.Plot(fig=fig, canvas=canvas, ax=ax)
quodplot.width = cfg['width']
quodplot.height = cfg['height']
for i, e in enumerate(entities):
if type(e) is quod.What:
e.set_style(i)
if name in cfg['color']:
e.set_tms_color(cfg['color'][name][i]['tms'])
e.set_curve_color(cfg['color'][name][i]['line'])
if 'linestyle' in cfg and name in cfg['linestyle']:
if i in cfg['linestyle'][name]: e.set_linestyle(cfg['linestyle'][name][i])
if 'linewidth' in cfg and name in cfg['linewidth']:
if i in cfg['linewidth'][name]: e.set_linewidth(cfg['linewidth'][name][i])
quodplot.add(e)
quodplot.render()
ax.set_xlabel(xlabel)
try: ax.set_title(cfg['titles'][name])
except KeyError: ax.set_title('')
if ylabel is not None: ax.set_ylabel(ylabel)
if yticks is not None: ax.set_yticks(yticks)
if name in cfg['xticks']:
xlim = ax.get_xlim()
ax.set_xticks(np.arange(xlim[0], xlim[1], cfg['xticks'][name]))
def quod_fragquod(frags,
fulls,
title,
outfile,
dpi=300,
width=30,
height=5.5,
kernel=None):
fig = quod.plt.figure()
ax = fig.add_subplot(111)
plot = quod.Plot(fig=fig, ax=ax)
plot.add(quod.FragmentWhat(frags[0], fulls[0], style=0, kernel=kernel))
plot.add(quod.FragmentWhat(frags[1], fulls[1], style=1, kernel=kernel))
correl, cov = plot[0].entdict['hydro'].get_correlation(
plot[1].entdict['hydro'])
plot.width = width
plot.height = height
plot.render()
plot.ax.set_title(title)
plot.fig.savefig(outfile, dpi=dpi)
return correl, cov
def entropy_quod(*sequences, **kwargs): '''This example plots the entropies of multiple sequences sequences: raw sequences **kwargs: outfile: where to put the resulting figure''' outfile = kwargs['outfile'] if 'outfile' in kwargs else kwargs['outfile'] plot = quod.Plot() for i, seq in enumerate(sequences): plot.add(quod.What(seq, style=i, mode='entropy')) plot.render() plot.save(outfile)
def colored_quod(seq1, seq2, linecolor1='red', linecolor2='blue', tmscolor1='orange', tmscolor2='cyan', outfile='test.png'): '''This example creates a standard hydropathy plot for two raw sequences, making sure to specify colors manually seq1: sequence 1 seq2: sequence 2 linecolor1: line color for sequence 1 linecolor2: line color for sequence 2 tmscolor1: tms color for sequence 1 tmscolor2: tms color for sequence 2 outfile: what to name the resulting figure''' plot = quod.Plot() plot.add(quod.What(seq1, tmscolor=tmscolor1, linecolor=linecolor1)) plot.add(quod.What(seq2, tmscolor=tmscolor2, linecolor=linecolor2)) plot.render() plot.save(outfile)
def simple_quod(*sequences, **kwargs):
'''This example creates a standard hydropathy plot from several raw sequences and saves it with a specific filename if given
*sequences: raw sequences
**kwargs:
window: window size for hydropathy averaging (default: 19)
outfile: what to name the resulting figure'''
outfile = 'test.png' if ('outfile' not in kwargs) else kwargs['outfile']
window = 19 if ('window' not in kwargs) else kwargs['window']
plot = quod.Plot()
for i, seq in enumerate(sequences):
plot.add(quod.What(seq, style=i, window=window))
plot.render()
plot.save(outfile)
def walls_quod(*sequences, **kwargs): '''This example plots sequences with walls+wedges defining certain intervals *sequences: raw sequences **kwargs: intervals: a list of Interval objects to generate walls+wedges from (default: []) outfile: what to name the resulting figure (default: test.png)''' plot = quod.Plot() intervals = [] if 'intervals' not in kwargs else kwargs['intervals'] outfile = 'test.png' if 'outfile' not in kwargs else kwargs['outfile'] mode = 'wall' if 'mode' not in kwargs else kwargs['mode'] for i in intervals: plot.add(i.get_auto()) for n, seq in enumerate(sequences): plot.add(quod.What(seq, style=n)) plot.render() plot.save(outfile)
def run(self):
print('Use [?] to get help on phoboshop shortcuts', file=sys.stderr)
self.fig = quod.plt.figure()
self.plot = quod.Plot(fig=self.fig)
for i, p in enumerate(self.proteins):
for e in p.render(style=i):
self.plot.add(e)
self.update_title()
self.plot.ax.figure.canvas.mpl_connect('button_press_event',
self.onmousedown)
self.plot.ax.figure.canvas.mpl_connect('button_release_event',
self.onmouseup)
self.plot.ax.figure.canvas.mpl_connect('motion_notify_event',
self.onmousemove)
self.plot.ax.figure.canvas.mpl_connect('key_press_event',
self.onkeydown)
#self.testline = self.plot.ax.plot([], [])
self.testline, = self.plot.ax.plot([], [])
self.plot.render()
quod.plt.show()
plt = quod.plt
sequences = []
for i, thing in enumerate(args.infiles):
if thing.startswith('asis:'):
sequences.append('>seq{}\n{}'.format(i + 1, thing[5:]))
else:
with open(thing) as f:
s = f.read()
if not s.startswith('>'):
sequences.append('>seq{}\n{}'.format(i + 1, s))
else:
sequences.append(s)
fig = plt.figure()
plot = quod.Plot(fig=fig)
n = 0
for i in range(0, len(sequences), 2):
x = quod.FragmentWhat(sequences[i],
sequences[i + 1],
style=n,
kernel=args.kernel)
plot.add(x)
whats.append(x)
n += 1
plot.render()
if args.correlate and (len(whats) > 1):
for i in range(len(whats)):
hydro1 = whats[i].entdict['hydro'].Y
for j in range(len(whats)):
def quod_set(seqids,
sequences,
indir,
outdir,
dpi=300,
force=False,
bars=[],
prefix='',
suffix='',
silent=False,
pars=[],
kernel=None):
''' generates QUOD plots for batches of sequences '''
if not os.path.isdir(outdir): os.mkdir(outdir)
#wedges = [[[x, 2 * (0.5 - (i % 2))] for i, x in enumerate(span)] for span in bars]
ove = lambda x: int(2 * (0.5 - (x % 2)))
wedges = []
for i, span in enumerate(bars):
wedges.append([])
if 1 <= i <= 2: y = -2
else: y = -2
wedges[-1].append(quod.Wall(spans=[span], y=y, ylim=[0, 0.5]))
medges = []
for i, span in enumerate(pars):
medges.append([])
y = 2
medges[-1].append(quod.Wall(spans=[span], y=y, ylim=[0.5, 1]))
domains = []
styledict = {}
for i, seqid in enumerate(seqids):
#if i < 2: color = 'red'
#else: color = 'blue'
#domains.append(parse_pfam('{}/../pfam/{}.pfam'.format(indir, seqid), color=color))
entities, styledict = parse_pfam('{}/../pfam/{}.pfam'.format(
indir, seqid),
styledict=styledict)
domains.append(entities)
#Draw A: barred by B
#quod.what([sequences[seqids[0]]], force_seq=True, title=seqids[0], imgfmt='png', outdir=outdir, outfile=(seqids[0] + '_' + seqids[1] + '.png'), dpi=dpi, hide=1, entities=wedges[0]+domains[0], silent=True, width=15, height=3)
halfwidth = 7.5
halfheight = 2
fig_a = quod.plt.figure()
ax_a = fig_a.add_subplot(111)
plot_a = quod.Plot(fig=fig_a, ax=ax_a)
plot_a.add(quod.What(sequences[seqids[0]], style=0, kernel=kernel))
for e in wedges[0] + domains[0]:
plot_a.add(e)
plot_a.width = halfwidth
plot_a.height = halfheight
plot_a.render()
plot_a.ax.set_title(seqids[0])
plot_a.fig.savefig('{}/{}_{}.png'.format(outdir, seqids[0], seqids[1]),
dpi=dpi)
#Draw B: barred by C
#quod.what([sequences[seqids[1]]], force_seq=True, title=seqids[1], imgfmt='png', outdir=outdir, outfile=(seqids[1] + '_' + seqids[2] + '.png'), dpi=dpi, hide=1, entities=wedges[1]+medges[0]+domains[1], silent=True, width=15, height=3)
fig_b = quod.plt.figure()
ax_b = fig_b.add_subplot(111)
plot_b = quod.Plot(fig=fig_b, ax=ax_b)
plot_b.add(quod.What(sequences[seqids[1]], style=0, kernel=kernel))
for e in wedges[1] + medges[0] + domains[1]:
plot_b.add(e)
plot_b.width = halfwidth
plot_b.height = halfheight
plot_b.render()
plot_b.ax.set_title(seqids[1])
plot_b.fig.savefig('{}/{}_{}.png'.format(outdir, seqids[1], seqids[2]),
dpi=dpi)
#Draw C: barred by B
#quod.what([sequences[seqids[2]]], force_seq=True, title=seqids[2], imgfmt='png', outdir=outdir, outfile=(seqids[2] + '_' + seqids[1] + '.png'), dpi=dpi, hide=1, color=1, entities=wedges[2]+medges[1]+domains[2], silent=True, width=15, height=3)
fig_c = quod.plt.figure()
ax_c = fig_c.add_subplot(111)
plot_c = quod.Plot(fig=fig_c, ax=ax_c)
plot_c.add(quod.What(sequences[seqids[2]], style=1, kernel=kernel))
for e in wedges[2] + medges[1] + domains[2]:
plot_c.add(e)
plot_c.width = halfwidth
plot_c.height = halfheight
plot_c.render()
plot_c.ax.set_title(seqids[2])
plot_c.fig.savefig('{}/{}_{}.png'.format(outdir, seqids[2], seqids[1]),
dpi=dpi)
#Draw D: barred by C
#quod.what([sequences[seqids[3]]], force_seq=True, title=seqids[3], imgfmt='png', outdir=outdir, outfile=(seqids[3] + '_' + seqids[2] + '.png'), dpi=dpi, hide=1, color=1, entities=wedges[3]+domains[3], silent=True, width=15, height=3)
fig_d = quod.plt.figure()
ax_d = fig_d.add_subplot(111)
plot_d = quod.Plot(fig=fig_d, ax=ax_d)
plot_d.add(quod.What(sequences[seqids[3]], style=1, kernel=kernel))
for e in wedges[3] + domains[3]:
plot_d.add(e)
plot_d.width = halfwidth
plot_d.height = halfheight
plot_d.render()
plot_d.ax.set_title(seqids[3])
plot_d.fig.savefig('{}/{}_{}.png'.format(outdir, seqids[3], seqids[2]),
dpi=dpi)
def plot(cfg, name, fig, ax, entities, xlabel=' ', ylabel=None, yticks=None):
quodplot = quod.Plot(fig=fig, ax=ax)
quodplot.width = cfg['width']
quodplot.height = cfg['height']
if name in cfg['xlim']: quodplot.xlim = cfg['xlim'][name]
if name in cfg['ylim']: quodplot.ylim = cfg['ylim'][name]
for i, e in enumerate(entities):
if quod.is_what(e):
e.set_style(i)
if (name in cfg['color']) and (i in cfg['color'][name]):
e.set_tms_color(cfg['color'][name][i]['tms'])
e.set_curve_color(cfg['color'][name][i]['line'])
if 'linestyle' in cfg and name in cfg['linestyle']:
if i in cfg['linestyle'][name]:
e.set_linestyle(cfg['linestyle'][name][i])
if 'linewidth' in cfg and name in cfg['linewidth']:
if i in cfg['linewidth'][name]:
e.set_linewidth(cfg['linewidth'][name][i])
else:
if avehas3 is not None:
if type(e) is avehas3.Avehas:
e.set_style(i)
if (name in cfg['color']) and (i in cfg['color'][name]):
e.entities[0].style = cfg['color'][name][i]['line']
e.entities[1].style = cfg['color'][name][i]['tms']
#if 'linestyle' in cfg and name in cfg['linestyle']:
# if i in cfg['linestyle'][name]: e.entities[0].linestyle = cfg['linestyle'][name][i]
#if 'linewidth' in cfg and name in cfg['linewidth']:
# if i in cfg['linewidth'][name]: e.entities[0].linewidth = cfg['linewidth'][name][i]
# if i in cfg['linewidth'][name]: e.entities[1].linewidth = cfg['linewidth'][name][i]
for prop in cfg:
#UNSTABLE!!!
if prop.startswith('linewidth') and name in cfg[prop]:
if '.' not in prop:
if i in cfg['linewidth'][name]:
e.entdict['hydro'].linewidth = cfg[
'linewidth'][name][i]
if i in cfg['linewidth'][name]:
e.entdict['amphi'].linewidth = cfg[
'linewidth'][name][i]
if i in cfg['linewidth'][name]:
e.entdict['simil'].linewidth = cfg[
'linewidth'][name][i]
else:
sp = prop.split('.')
rootprop = sp[0]
if sp[1] == 'simil':
e.linewidthsimil = cfg[prop][name][i]
elif sp[1] == 'amphi':
e.linewidthamphi = cfg[prop][name][i]
if prop.startswith('linestyle') and name in cfg[prop]:
if '.' not in prop:
if i in cfg['linestyle'][name]:
e.entities[0].linestyle = cfg['linestyle'][
name][i]
else:
sp = prop.split('.')
rootprop = sp[0]
if sp[1] == 'simil':
e.linestylesimil = cfg[prop][name][i]
elif sp[1] == 'amphi':
e.linestyleamphi = cfg[prop][name][i]
quodplot.add(e)
quodplot.render()
ax.set_xlabel(xlabel)
#ax.set_title(cfg['title'].get(name, ''), fontsize=get_titlefont(cfg, name))
ax.set_title('')
if ylabel is not None: ax.set_ylabel(ylabel)
if yticks is not None: ax.set_yticks(yticks)
if name in cfg['xticks']:
xlim = ax.get_xlim()
ax.set_xticks(np.arange(xlim[0], xlim[1], cfg['xticks'][name]))
