def render(self, style=0):
self.what = quod.What(self.get_sequence(), style=style)
self.entities['what'] = self.what
entlist = []
entlist = [self.what.entities[0]]
return entlist
def render(self, style=0):
what = quod.What(self.get_sequence(), style=style)
self.entities['what'] = what
entlist = []
for k in self.entities:
entlist.append(self.entities[k])
return entlist
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 render(self, style=0):
for msa in self.alignments:
self.what = quod.What('', style=style, nohmmtop=True)
self.hydro = self.what.entities[0]
self.hydro.Y = avehas3.get_average_hydropathies(msa, window=19)
self.hydro.X = np.arange(0., len(self.hydro.Y))
self.entities['what'] = self.what
entlist = []
entlist = [self.what.entities[0]]
if self.amphipathicity:
amphi = quod.Hydropathy('', style='g')
amphi.Y = avehas3.get_average_amphipathicities(msa, window=19)
amphi.X = np.arange(0, len(amphi.Y))
entlist.append(amphi)
entlist.append(
avehas3.TMcenter(avehas3.get_tmcenters(msa),
ymin=-3,
ymax=-2.4))
simil = avehas3.get_similarities(msa)
window = 10
ymin = -3
ymax = -1.5
scores = np.array([
np.nanmean(simil[i:i + window])
for i in range(0,
len(simil) - window)
])
normscores = (scores - min(scores)) / (max(scores) - min(scores))
scaledscores = normscores * (ymax - ymin)
shiftedscores = scaledscores + ymin
similcurve = quod.Hydropathy('', style='gray')
similcurve.Y = shiftedscores
similcurve.X = np.arange(0, len(shiftedscores)) + window // 2
entlist.append(similcurve)
if self.occupancy:
occcurve = quod.Hydropathy('', style='y')
occcurve.Y = avehas3.get_occupancies(msa)
occcurve.X = np.arange(len(occcurve.Y))
entlist.append(occcurve)
#what's the worst that can happen???
return entlist
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 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_quod(cfg):
entities = {}
maxlens = {}
for name in cfg['subplots']:
entities[name] = []
maxlens[name] = 0
for seq in cfg['sequences'][name]:
entities[name].append(quod.What(seq))
maxlens[name] = max(maxlens[name], len(entities[name][-1]))
#walls
if name in cfg['walls']:
for walldef in cfg['walls'][name]:
entities[name].append(quod.Wall(spans=[[walldef['start'], walldef['end']]], y=walldef['y'], ylim=walldef['lim'], thickness=walldef['thickness'], wedge=walldef['thickness']))
#domains
if name in cfg['domains']:
for domaindef in cfg['domains'][name]:
entities[name].append(quod.Region(
spans=domaindef['xlim'],
yspan=domaindef['ylim'],
label=domaindef['label'],
style=domaindef['color'],
pos=domaindef['pos'],
size=domaindef['fontsize'],
center=domaindef['halign']
))
cfg['weights'][name] *= maxlens[name]
if 'tms' in cfg: do_tms_stuff(entities, cfg)
fig = Figure()
canvas = FigureCanvas(fig)
fig.set_tight_layout(True)
gs = gridspec.GridSpec(len(cfg['rowscheme']), cfg['hres'])
hgap = cfg['hgap']/cfg['width']/2
margin = 0.03 if 'margin' not in cfg else cfg['margin']
gs.update(
left=margin + hgap,
right=cfg['width'] - margin,
top=cfg['height'] - margin-hgap,
bottom=margin, wspace=0)
def get_limit(wt1, wtlist, offset=0):
x = int((offset + wt1/sum(wtlist)) * cfg['hres'])
return max(0, min(x, cfg['hres']))
if cfg['mode'] == 'hvordan':
lims = []
cfg['lims'] = {}
for namelist in cfg['rowscheme']:
row = [cfg['weights'][name] for name in namelist]
last = -hgap
if len(namelist) == 1:
cfg['lims'][namelist[0]] = [0, cfg['hres']]
else:
bounds = [0]
s = 0
rawweights = [cfg['weights'][name] for name in namelist]
weights = [w/sum(rawweights) for w in rawweights]
for i in range(len(namelist) - 1):
bounds.append((weights[i] - hgap) * cfg['hres'])
bounds.append((weights[i] + hgap) * cfg['hres'])
#for i in namelist
bounds.append(cfg['hres'])
bounds = [int(x) for x in bounds]
for i in range(0, len(namelist)):
name = namelist[i]
cfg['lims'][name] = [bounds[2*i], bounds[2*i + 1]]
axdict = {}
for r, row in enumerate(cfg['rowscheme']):
for name in row:
#axdict[name] = fig.add_subplot(gs[r, cfg['lims'][name][0]:cfg['lims'][name][1]])
axdict[name] = fig.add_subplot(gs[r,cfg['lims'][name][0]:cfg['lims'][name][1]])
n = 0
name2row = {}
stretchlabel = {}
firstcol = set()
for r, row in enumerate(cfg['rowscheme']):
for c, name in enumerate(row):
if not c: firstcol.add(name)
name2row[name] = r
if 'ylabel' in cfg and name in cfg['ylabel']: ylabel = cfg['ylabel'][name]
else: ylabel = '' if c else None
yticks = [] if c else None
plot(cfg, name, fig, canvas, axdict[name], entities[name], ylabel=ylabel, yticks=yticks)
try: title = cfg['title'][name]
except KeyError: title = chr(65 + n)
axdict[name].set_title(title, loc='left')
n += 1
if len(row) > 1:
ax = fig.add_subplot(gs[r,:])
ax.set_xticks([0])
ax.axes.get_yaxis().set_visible(False)
ax.set_frame_on(False)
#TODO: expose customizing xlabels per-plot/per-row
ax.set_xlabel('Position')
ax.tick_params(labelcolor=(0,0,0,0), color=(0,0,0,0))
stretchlabel[r] = ax
elif len(row) == 1:
#ax = fig.add_subplot(gs[r,:])
ax = axdict[row[0]]
ax.set_xlabel('Position')
stretchlabel[r] = ax
if 'xlabel' in cfg:
for name in cfg['xlabel']:
stretchlabel[name2row[name]].set_xlabel(cfg['xlabel'][name])
if 'ylabel' in cfg:
for name in cfg['ylabel']:
stretchlabel[name2row[name]].set_ylabel(cfg['ylabel'][name])
if 'font' in cfg:
for name in cfg['font']:
for target in cfg['font'][name]:
if target.endswith('ticks'):
axdict[name].tick_params(labelsize=cfg['font'][name][target])
if name in firstcol:
stretchlabel[name2row[name]].tick_params(labelsize=cfg['font'][name][target])
elif target.endswith('xaxis'):
axdict[name].set_xlabel(axdict[name].get_xlabel(),
fontsize=cfg['font'][name][target])
stretchlabel[name2row[name]].set_xlabel(stretchlabel[name2row[name]].get_xlabel(),
fontsize=cfg['font'][name][target])
elif target.endswith('yaxis'):
axdict[name].set_ylabel(axdict[name].get_ylabel(),
fontsize=cfg['font'][name][target])
elif target == 'title':
axdict[name].set_title(axdict[name].get_title(),
fontsize=cfg['font'][name][target])
#gs.tight_layout(fig, pad=cfg['margin'], w_pad=cfg['hgap'], h_pad=0.0)
gs.tight_layout(fig, pad=0, w_pad=cfg['hgap'], h_pad=cfg['vgap'])
fig.savefig(cfg['outfile'], dpi=cfg['dpi'])
else: raise NotImplementedError('Unimplemented mode: {}'.format(cfg['mode']))
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 run_quod(cfg):
entities = {}
maxlens = {}
for name in cfg['subplots']:
entities[name] = []
maxlens[name] = 0
mode = cfg['mode'][name]
if mode in ('hvordan', 'quod'):
if cfg['frag'][name]:
for i in range(0, len(cfg['sequences'][name]), 2):
entities[name].append(
quod.FragmentWhat(cfg['sequences'][name][i],
cfg['sequences'][name][i + 1]))
maxlens[name] = max(maxlens[name], len(entities[name][-1]))
else:
for seq in cfg['sequences'][name]:
entities[name].append(quod.What(seq))
maxlens[name] = max(maxlens[name], len(entities[name][-1]))
elif mode in ('avehas', ):
if avehas3 is None: raise ImportError('Could not find avehas3.py')
for seq in cfg['sequences'][name]:
entities[name].append(
avehas3.Avehas(io.BytesIO(seq.encode('utf-8')),
amphi=cfg['amphi'][name]))
#print(name, seq, maxlens[name])
#for msa in avehas3.AlignIO.parse(
#print(len(entities[name][-1]))
maxlens[name] = max(maxlens[name], len(entities[name][-1]))
elif mode in ('empty', ):
spacer = Spacer(length=cfg['baselength'][name])
maxlens[name] = cfg['baselength'][name]
entities[name].append(spacer)
for seq in cfg['sequences'][name]:
#walls
if name in cfg['walls']:
for walldef in cfg['walls'][name]:
entities[name].append(
quod.Wall(spans=[[walldef['start'], walldef['end']]],
y=walldef['y'],
ylim=walldef['lim'],
thickness=walldef['thickness'],
wedge=walldef['thickness']))
#domains
if name in cfg['domains']:
for domaindef in cfg['domains'][name]:
entities[name].append(
quod.Region(spans=domaindef['xlim'],
yspan=domaindef['ylim'],
label=domaindef['label'],
style=domaindef['color'],
pos=domaindef['pos'],
size=domaindef['fontsize'],
center=domaindef['halign']))
if name in cfg['text']:
label = cfg['text'][name]
entities[name].append(
quod.Text(label['pos'], label['text'],
label.get('halign', 'l'), label.get('font', None)))
if cfg['baselength'][name] is None:
cfg['baselength'][name] = maxlens[name]
#cfg['length'][name] = maxlens[name]
#cfg['weight'][name] = maxlens[name]
cfg['length'][name] = cfg['baselength'][name] * cfg['weight'][name]
if 'tms' in cfg: do_tms_stuff(entities, cfg)
fig = quod.Figure()
fig.set_tight_layout(True)
gs = gridspec.GridSpec(len(cfg['rowscheme']), cfg['hres'])
hgap = cfg['hgap'] / cfg['width'] / 2
margin = 0.03 if 'margin' not in cfg else cfg['margin']
gs.update(left=margin + hgap,
right=cfg['width'] - margin,
top=cfg['height'] - margin - hgap,
bottom=margin,
wspace=0)
def get_limit(wt1, wtlist, offset=0):
x = int((offset + wt1 / sum(wtlist)) * cfg['hres'])
return max(0, min(x, cfg['hres']))
if True:
lims = []
cfg['lims'] = {}
for namelist in cfg['rowscheme']:
row = [cfg['length'][name] for name in namelist]
last = -hgap
if len(namelist) == 1:
cfg['lims'][namelist[0]] = [0, cfg['hres']]
else:
bounds = [0]
s = 0
rawweight = [cfg['length'][name] for name in namelist]
weight = [w / sum(rawweight) for w in rawweight]
for i in range(len(namelist) - 1):
bounds.append((weight[i] - hgap) * cfg['hres'])
bounds.append((weight[i] + hgap) * cfg['hres'])
#for i in namelist
bounds.append(cfg['hres'])
bounds = [int(x) for x in bounds]
for i in range(0, len(namelist)):
name = namelist[i]
cfg['lims'][name] = [bounds[2 * i], bounds[2 * i + 1]]
axdict = {}
for r, row in enumerate(cfg['rowscheme']):
for name in row:
#axdict[name] = fig.add_subplot(gs[r, cfg['lims'][name][0]:cfg['lims'][name][1]])
axdict[name] = fig.add_subplot(
gs[r, cfg['lims'][name][0]:cfg['lims'][name][1]])
n = 0
name2row = {}
stretchlabel = {}
firstcol = set()
for r, row in enumerate(cfg['rowscheme']):
for c, name in enumerate(row):
if not c: firstcol.add(name)
name2row[name] = r
if 'ylabel' in cfg and name in cfg['ylabel']:
ylabel = cfg['ylabel'][name]
else:
ylabel = '' if c else None
yticks = None #[] if c else None
plot(cfg,
name,
fig,
axdict[name],
entities[name],
ylabel=ylabel,
yticks=yticks)
if c:
axdict[name].set_yticklabels(
[] * len(axdict[name].get_yticklabels()))
try:
title = cfg['title'][name]
except KeyError:
title = chr(65 + n)
titlefont = get_titlefont(cfg, name)
#TODO: implement rowtitle separately
#axdict[name].set_title(cfg['title'].get(name, ''), loc='left', fontsize=titlefont)
titlepad = quod.matplotlib.rcParams['axes.titlepad']
transOffset = matplotlib.transforms.ScaledTranslation(
0., titlepad / 72., fig.dpi_scale_trans)
if name in cfg['ctitle']:
subtitlefont = get_titlefont(cfg,
name,
subname='ctitle',
default=titlefont)
t = axdict[name].text(0.5,
1.0,
cfg['ctitle'].get(name, ''),
ha='center',
va='baseline',
fontsize=subtitlefont,
transform=axdict[name].transAxes)
t.set_transform(axdict[name].transAxes + transOffset)
if name in cfg['ltitle']:
subtitlefont = get_titlefont(cfg,
name,
subname='ltitle',
default=titlefont)
t = axdict[name].text(0.0,
1.0,
cfg['ltitle'].get(name, ''),
ha='left',
va='baseline',
fontsize=subtitlefont,
transform=axdict[name].transAxes)
t.set_transform(axdict[name].transAxes + transOffset)
if name in cfg['rtitle']:
subtitlefont = get_titlefont(cfg,
name,
subname='rtitle',
default=titlefont)
t = axdict[name].text(1.0,
1.0,
cfg['rtitle'].get(name, ''),
ha='right',
va='baseline',
fontsize=subtitlefont,
transform=axdict[name].transAxes)
t.set_transform(axdict[name].transAxes + transOffset)
if name in cfg['title']:
axdict[name].set_title(cfg['title'].get(name, ''),
loc='left',
fontsize=titlefont)
n += 1
if len(row) > 1:
ax = fig.add_subplot(gs[r, :])
ax.set_xticks([0])
ax.axes.get_yaxis().set_visible(False)
#ax.axes.get_xaxis().set_visible(False)
ax.set_frame_on(False)
#TODO: expose customizing xlabels per-plot/per-row
ax.set_xlabel('Position')
ax.tick_params(labelcolor=(1, 1, 1, 0), color=(1, 1, 1, 0))
for side in ['left', 'right', 'bottom', 'top']:
ax.spines[side].set_color((1, 1, 1, 0))
ax.spines[side].set_linewidth(0)
stretchlabel[r] = ax
elif len(row) == 1:
#ax = fig.add_subplot(gs[r,:])
ax = axdict[row[0]]
ax.set_xlabel('Position')
stretchlabel[r] = ax
if 'xlabel' in cfg:
for name in cfg['xlabel']:
if name.startswith('row:'):
stretchlabel[name2row[name[4:]]].set_xlabel(
cfg['xlabel'][name])
else:
axdict[name].set_xlabel(cfg['xlabel'][name])
stretchlabel[name2row[name]].set_xlabel(' ')
if 'ylabel' in cfg:
for name in cfg['ylabel']:
stretchlabel[name2row[name]].set_ylabel(cfg['ylabel'][name])
if 'font' in cfg:
for name in cfg['font']:
for target in cfg['font'][name]:
if target.endswith('ticks'):
axdict[name].tick_params(
labelsize=cfg['font'][name][target])
if name in firstcol:
stretchlabel[name2row[name]].tick_params(
labelsize=cfg['font'][name][target])
elif target.endswith('xaxis'):
axdict[name].set_xlabel(
axdict[name].get_xlabel(),
fontsize=cfg['font'][name][target])
stretchlabel[name2row[name]].set_xlabel(
stretchlabel[name2row[name]].get_xlabel(),
fontsize=cfg['font'][name][target])
elif target.endswith('yaxis'):
axdict[name].set_ylabel(
axdict[name].get_ylabel(),
fontsize=cfg['font'][name][target])
#gs.tight_layout(fig, pad=cfg['margin'], w_pad=cfg['hgap'], h_pad=0.0)
#gs.tight_layout(fig, pad=0, w_pad=cfg['hgap'], h_pad=cfg['vgap'])
gs.tight_layout(fig,
pad=cfg['margin'],
w_pad=cfg['hgap'],
h_pad=cfg['vgap'])
fig.savefig(cfg['outfile'], dpi=cfg['dpi'])
else:
raise NotImplementedError('Unimplemented mode: {}'.format(cfg['mode']))