class HistPlotTheme(PlotTheme):
"cycles & peaks plot theme: histogram"
name = "cyclehist.plot.hist"
figsize = (
AppTheme().appsize[0] - CyclePlotTheme.figsize[0], # pylint: disable=unsubscriptable-object
*CyclePlotTheme.figsize[1:])
xlabel = PeaksPlotTheme.xlabel
ylabel = CyclePlotTheme.ylabel
explabel = 'Hybridisations'
reflabel = 'Hairpin'
formats = {'bases': '0.0a', 'ref': '0', 'exp': '0.0'}
hist = deepcopy(PeaksPlotTheme.count)
events = PlotAttrs(hist.color,
'o',
4,
alpha=.25,
selection_alpha=1.,
selection_color='~green')
peaks = PlotAttrs(hist.color, '△', 5, alpha=0., angle=np.pi / 2.)
pkcolors = deepcopy(PeaksPlotTheme.pkcolors)
minzoomz: Optional[float] = .008 / .88e-3
toolbar = dict(CyclePlotTheme.toolbar)
toolbar['items'] = 'pan,box_zoom,wheel_zoom,hover,reset,save'
tooltipmode = 'hline'
tooltippolicy = 'follow_mouse'
tooltips = [(i[1], '@' + i[0] + ("{" + i[2] + "}" if i[2] else ""))
for i in PeakListTheme().columns[1:-1]]
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class CyclesPlotTheme(PlotTheme):
"theme for cycles"
name = "cycles.plot"
raw = PlotAttrs('color',
'o',
.1,
alpha=.5,
palette={
'dark': 'YlOrBr',
'basic': 'inferno'
})
selection = {
'dark': PlotAttrs('lightblue', 'line', 3),
'basic': PlotAttrs('blue', 'line', 3)
}
tooltips = [('(cycle, t, z)', '(@cycle, $~x{1}, $data_y{1.1111})')]
radius = 1.
histframes = PlotAttrs('~gray', '┸', 1, fill_color='gray')
histcycles = PlotAttrs('~blue', '┸', 1, fill_color=None, line_alpha=.5)
histxtoplabel = 'Cycles'
histxlabel = 'Frames'
figsize = PlotTheme.defaultfigsize(450, 450)
toolbar = dict(PlotTheme.toolbar)
toolbar.update(raw='tap,ypan,ybox_zoom,reset,save,dpxhover',
items='ypan,ybox_zoom,reset,save')
@initdefaults(frozenset(locals()))
def __init__(self, **kwa):
super().__init__(**kwa)
class DriftControlPlotTheme(PlotTheme):
"drift control plot theme"
name = "qc.driftcontrol.plot"
measures = PlotAttrs('', '-', 2, alpha=.75)
median = PlotAttrs('', '-', 2, line_dash='dashed')
pop10 = PlotAttrs('', '-', 2, line_dash=[4])
pop90 = PlotAttrs('', '-', 2, line_dash=[4])
colors = dict(dark=dict(measures='lightblue',
median='lightgreen',
pop10='lightgreen',
pop90='lightgreen'),
basic=dict(measures='darkblue',
median='darkgreen',
pop10='darkgreen',
pop90='darkgreen'))
figsize = PlotTheme.defaultfigsize(300, 150)
outlinewidth = 7
outlinecolor = 'red'
outlinealpha = .5
ylabel = ''
xlabel = 'Cycles'
toolbar = dict(PlotTheme.toolbar)
toolbar['items'] = 'pan,box_zoom,reset,save'
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class PeaksPlotTheme(PlotTheme):
"""
peaks plot theme
"""
name = "hybridstat.peaks.plot"
figsize = PlotTheme.defaultfigsize(300, 500)
xtoplabel = 'Duration (s)'
xlabel = 'Rate (%)'
fiterror = "Fit unsuccessful!"
ntitles = 4
count = PlotAttrs('~blue', '-', 1)
eventscount = PlotAttrs(count.color, 'o', 3)
peakscount = PlotAttrs(count.color,
'△',
15,
fill_alpha=0.5,
angle=np.pi / 2.)
referencecount = PlotAttrs('bisque', 'patch', alpha=0.5)
peaksduration = PlotAttrs('~green',
'◇',
15,
fill_alpha=0.5,
angle=np.pi / 2.)
pkcolors = dict(dark=dict(reference='bisque', missing='red',
found='black'),
basic=dict(reference='bisque', missing='red',
found='gray'))
toolbar = dict(PlotTheme.toolbar)
toolbar['items'] = 'ypan,ybox_zoom,ywheel_zoom,reset,save,tap'
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class HairpinGroupScatterTheme(PlotTheme):
"grouped beads plot theme"
name = "hairpingroup.plot"
figsize = PlotTheme.defaultfigsize(500, 300)
xlabel = 'Bead'
ylabel = 'Bases'
reflabel = 'Hairpin'
xgridalpha = 0.
ntitles = 5
format = '0.0'
events = PlotAttrs('~gray', 'o', 3, alpha=.5)
peaks = PlotAttrs('~blue', 'o', 10, line_alpha=1., fill_alpha=.0)
hpin = PlotAttrs('color', '+', 15, alpha=1., line_width=2)
pkcolors = {
'dark': {
'missing': 'red',
'found': 'lightgreen'
},
'basic': {
'missing': 'red',
'found': 'darkgreen'
}
}
toolbar = dict(PlotTheme.toolbar)
toolbar['items'] = 'pan,box_zoom,reset,save,hover,box_select'
tooltipmode = 'mouse'
tooltippolicy = 'follow_mouse'
tooltips = [('Bead', '@bead'), ('Z (base)', '@bases'),
('Ref (base)', '@id'), (PeaksPlotTheme.xlabel, '@count{0.0}'),
(PeaksPlotTheme.xtoplabel, '@duration{0.000}')]
displaytimeout = .5
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class ExtensionPlotTheme(DriftControlPlotTheme):
"drift control plot theme"
name = "qc.extension.plot"
ylabel = 'δ(Φ3-Φ1) (µm)'
measures = PlotAttrs('', 'o', 2, alpha=.75)
ybars = PlotAttrs('', 'vbar', 1, alpha=.75)
ymed = PlotAttrs('', 'vbar', 1, fill_alpha=0.)
colors = dict(DriftControlPlotTheme.colors)
colors['dark'].update(ybars='lightblue', ymed='lightblue')
colors['basic'].update(ybars='darkblue', ymed='darkblue')
ybarswidth = .8
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class ConsensusScatterTheme(PlotTheme):
"scatter plot of durations & rates thee"
name = "consensus.plot.scatter"
figsize = PlotTheme.defaultfigsize(300, 300)
xlabel = PeaksPlotTheme.xlabel
ylabel = PeaksPlotTheme.xtoplabel
reflabel = 'Hairpin'
format = '0.0'
peaks = PlotAttrs('color', '+', 10, line_alpha=1., fill_alpha=.0)
pkcolors = {
'dark': {
'missing': 'red',
'found': 'lightgreen'
},
'basic': {
'missing': 'red',
'found': 'darkgreen'
}
}
toolbar = dict(PlotTheme.toolbar)
toolbar['items'] = 'pan,box_zoom,reset,save,hover,box_select'
tooltipmode = 'mouse'
tooltippolicy = 'follow_mouse'
tooltips = [('Bead', '@bead'), ('Z (base)', '@bases'),
('Strand', '@orient'), (PeaksPlotTheme.xlabel, '@rate{0.0}'),
(PeaksPlotTheme.xtoplabel, '@duration{0.000}')]
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class FoVPlotTheme(PlotTheme):
"FoV plot theme"
name = "fov"
beads = PlotAttrs('color',
'o',
alpha=.7,
nonselection_alpha=.7,
selection_alpha=.7,
nonselection_color='color',
selection_fill_color='color')
text = PlotAttrs('color',
'text',
text_font_style='bold',
nonselection_alpha=1.,
nonselection_text_color="color",
selection_alpha=1.,
selection_text_color='blue')
image = PlotAttrs('Greys256', 'image', x=0, y=0)
radius = 1.
figsize = PlotTheme.defaultfigsize(160 * 5, 100 * 5)
calibfigsize = PlotTheme.defaultfigsize(256, 192)
ylabel = 'Y (μm)'
xlabel = 'X (μm)'
colors = dict(ok='palegreen',
fixed='chocolate',
bad='orange',
discarded='red',
missing='magenta')
thumbnail = 128
calibimg = PlotAttrs('Greys256', 'image', x=0, y=0)
calibsize = 6. / 16
tooltips = '<table>@ttips{safe}</table>'
tooltiptype = dict(NAMES)
tooltiprow = ('<tr>' + '<td>{cycle}</td><td>cycle{plural} with:</td>' +
'<td>{type}</td><td>{message}</td>' + '</tr>')
tooltipok = ('<tr><td><td><td>σ[HF] =</td><td>{:.4f}</td></tr>'
'<tr><td><td><td>Δz =</td><td>{:.2f}</td></tr>')
toolbar = dict(PlotTheme.toolbar)
toolbar['items'] = 'pan,box_zoom,reset,tap,save,hover'
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class CyclePlotTheme(PlotTheme):
"cycles & peaks plot theme: cycles"
name: str = "cyclehist.plot.cycle"
figsize: Tuple[int, int, str] = (300, 497, 'fixed')
phasezoom: int = 20
fiterror: str = PeaksPlotTheme.fiterror
xlabel: str = PlotTheme.xtoplabel
ylabel: str = PlotTheme.yrightlabel
ntitles: int = 5
format: str = '0.0a'
frames: PlotAttrs = PlotAttrs('~gray', '-', 1., alpha=.25)
points: PlotAttrs = PlotAttrs(deepcopy(PeaksPlotTheme.count.color),
'o',
1,
alpha=.5)
toolbar: Dict[str, Any] = dict(PlotTheme.toolbar,
items='pan,box_zoom,wheel_zoom,reset,save')
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class RampPlotTheme(PlotTheme):
"""
ramp plot theme
"""
name = "ramp.theme"
consensusarea = PlotAttrs('~gray', 'patch', 1, alpha=.5)
consensusline = PlotAttrs(consensusarea.color, 'line', 1, alpha=.5)
beadarea = PlotAttrs('~blue', 'patch', 1, alpha=.5)
beadline = PlotAttrs(beadarea.color, 'line', 1, alpha=.5)
beadcycles = PlotAttrs(beadarea.color, 'line', 1, alpha=.5)
frames = PlotAttrs("phase", 'o', 5, alpha=.25)
phases = ['lightblue'] * 5 + ['darkgreen'] * 4
phaserange = (..., ...)
ylabelnormalized = "Z (% strand size)"
xlabel = 'Z magnet (mm)'
figsize = PlotTheme.defaultfigsize(300, 500)
widgetwidth = 500
dataformat = "raw"
clip = 99., .1
toolbar = dict(PlotTheme.toolbar)
toolbar['items'] = 'pan,box_zoom,reset,save'
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class CleaningPlotTheme(PlotTheme):
"""
cleaning plot theme
"""
name: str = "cleaning.theme"
lines: PlotAttrs = PlotAttrs('~gray', '-', 1, alpha=.3)
points: PlotAttrs = PlotAttrs('color', 'o', 1, alpha=.5)
hover: PlotAttrs = PlotAttrs('white', 'o', 4, alpha=0.)
figsize: Tuple[int, int, str] = PlotTheme.defaultfigsize(300, 500)
clip: int = 3
clipovershoot: float = 10
maxfixedbeads: int = 15
widgetwidth: int = 535
ntitles: int = 5
order: Tuple[str, ...] = ('aberrant', 'hfsigma', 'extent', 'population',
'pingpong', 'alignment', 'clipping',
'saturation', 'good')
colors: Dict[str, str] = dict(
good='#6baed6', # blue
hfsigma='gold',
extent='orange',
population='hotpink',
pingpong='firebrick',
saturation='chocolate',
alignment='darkgray',
clipping='darkorchid',
aberrant='red')
tooltips: List[Tuple[str, ...]] = [
('(cycle, t, z, status)', '(@cycle, $~x{1}, $data_y{1.1111}, @status)')
]
toolbar: Dict[str, Any] = dict(
PlotTheme.toolbar,
items='pan,box_zoom,ypan,ybox_zoom,ywheel_zoom,reset,save,dpxhover')
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class HairpinGroupHistTheme(PlotTheme):
"grouped beads plot theme"
name = "hairpingroup.plot.hist"
figsize = PlotTheme.defaultfigsize(300, 300)
xdata = "duration"
binsize = .1
xlabel = PeaksPlotTheme.xtoplabel
ylabel = 'Density'
hist = PlotAttrs('~gray', '┸', 1, fill_color='gray')
toolbar = dict(PlotTheme.toolbar)
toolbar['items'] = 'pan,box_zoom,reset,save'
@initdefaults(frozenset(locals()))
def __init__(self, **_):
super().__init__(**_)
class BeadsScatterPlotConfig(BasePlotConfig):
"Information about the current fovs displayed"
name: str = NAME
sorting: Set[str] = field(
default_factory=lambda: {'hairpin', 'track', 'bead'})
figargs: Dict[str, Any] = field(default_factory=lambda: dict(
toolbar_sticky=False,
toolbar_location='above',
tools=['pan,wheel_zoom,box_zoom,save,reset,hover'],
plot_width=1000,
plot_height=600,
sizing_mode=defaultfigsize()[-1],
x_axis_label='bead'))
yaxis: Tuple[str, str] = ("postions (base pairs = {:.2f} nm⁻¹)",
"positions (base pairs)")
datacolumns: List[str] = field(default_factory=lambda: [
'hybridisationrate', 'averageduration', 'blockageresolution',
'baseposition', 'peakposition', 'status', 'distance', 'closest',
'orientation', 'hairpin'
])
tooltipcolumns: List[Tuple[str, str]] = field(
default_factory=lambda: [(getcolumn(i).label if i != 'baseposition'
else 'z (bp)', f'@{i}') for i in (
'hybridisationrate',
'averageduration',
'blockageresolution',
'status',
'distance',
'closest',
'orientation',
)])
events: PlotAttrs = field(default_factory=lambda: PlotAttrs(
'',
'oval',
fill_color='~gray',
fill_alpha=.5,
line_alpha=1.,
line_width=2.,
line_color='color',
x='x',
y='baseposition',
width='hybridisationrate',
height='blockageresolution',
))
blockages: PlotAttrs = field(default_factory=lambda: PlotAttrs(
'color',
'o',
10,
x='x',
y='baseposition',
fill_alpha=0.,
line_alpha=0.,
))
bindings: PlotAttrs = field(default_factory=lambda: PlotAttrs(
'color', 'x', 10, x='x', y='bindingposition', alpha=.8))
colors: Dict[str, str] = field(
default_factory=lambda: {
"truepos": "lightgreen",
"falsepos": "red",
"falseneg": "red",
"baseline": "dpxblue",
"< baseline": "dpxblue",
"singlestrand": "dpxblue",
"> singlestrand": "dpxblue",
"": "lightgreen"
})
order: Dict[str, int] = field(
default_factory=lambda: {
j: i
for i, j in enumerate(
("baseline", "< baseline", "singlestrand", "> singlestrand",
"", "truepos", "falsepos", "falseneg"))
})
class FoVStatsPlotConfig(BasePlotConfig):
"Information about the current fovs displayed"
name: str = NAME
linear: bool = True
refagg: str = 'median'
yaxisnorm: YAxisNorm = field(
default_factory=lambda: ("status", ["", "truepos"]))
binnedz: BinnedZ = field(default_factory=BinnedZ)
binnedbp: BinnedZ = field(default_factory=lambda: BinnedZ(10, 10, 0))
xinfo: List[AxisConfig] = field(
default_factory=lambda:
[AxisConfig('track'), AxisConfig('beadstatus')])
yaxis: str = 'bead'
xaxistag: Dict[str, str] = field(
default_factory=lambda:
{i.key: str(i.label)
for i in COLS if (i.axis == 'x') and i.label})
yaxistag: Dict[str, str] = field(
default_factory=lambda:
{i.key: str(i.label)
for i in COLS if (i.axis == 'y') and i.label})
orientationtag: Dict[str, str] = field(default_factory=lambda: {
"+": "+",
"-": INVISIBLE + "-",
"": INVISIBLE * 2 + '?'
})
uselabelcolors: bool = True
defaultcolors: str = 'Blues'
orientationcolor: Dict[str, str] = field(default_factory=lambda: {
"+": "lightgreen",
"-": "dpxblue"
})
statuscolor: Dict[str, str] = field(
default_factory=lambda: {
"< baseline": f"dpxblue",
"baseline": f"dpxblue",
"truepos": f"lightgreen",
"falseneg": f"red",
"falsepos": f"red",
"": f"green",
"singlestrand": f"dpxblue",
"> singlestrand": f"dpxblue",
})
beadstatuscolor: Dict[str, str] = field(
default_factory=lambda: {
"ok": "lightgreen",
**dict.fromkeys(("empty", "bug", "unknown"), "red"),
**dict.fromkeys(_ExceptionNames.keys(), "red")
})
spread: float = 1.5
toplabel: Tuple[str, str] = ('Bead count', 'Bead / Blockage count')
toptick: Tuple[str, str] = ('{}', '{}/{}')
figargs: Dict[str, Any] = field(default_factory=lambda: dict(
toolbar_sticky=False,
toolbar_location='above',
tools=['pan,wheel_zoom,box_zoom,save,reset,hover'],
plot_width=900,
plot_height=400,
sizing_mode=defaultfigsize()[-1],
))
pointstips: List[Tuple[str, str]] = field(default_factory=lambda: [
("track", "@track"),
("bead", "@bead"),
("y", "$y"),
])
boxtips: List[Tuple[str, str]] = field(default_factory=lambda: [
("x", "@xv"),
("y", "@yv"),
])
box: PlotAttrs = field(default_factory=lambda: PlotAttrs(
'',
'rect',
fill_color='color',
line_color='color',
x='x',
y=f'boxcenter',
width=.9,
height=f'boxheight',
))
vertices: PlotAttrs = field(default_factory=lambda: PlotAttrs(
'',
'segment',
line_color='dpxblue',
line_width=2,
x0='x',
x1='x',
y0=f'bottom',
y1=f'top',
))
median: PlotAttrs = field(default_factory=lambda: PlotAttrs(
'',
'rect',
fill_color='black',
line_color='black',
x='x',
y='median',
height=.00001,
line_width=1,
width=.9,
))
bars: PlotAttrs = field(default_factory=lambda: PlotAttrs(
'',
'rect',
fill_color='dpxblue',
line_color='dpxblue',
x='x',
height=.00001,
line_width=3,
width=.5,
))
points: PlotAttrs = field(default_factory=lambda: PlotAttrs(
'~gray', 'circle', x='x', y='y', size=10))
@property
def xaxis(self) -> List[str]:
"return x-axis names"
return [i.name for i in self.xinfo]
def getxaxisinfo(self, attr: str, xaxis: List[Union[str,
AxisConfig]]) -> list:
"x axis info"
vals = {getattr(j, 'name', j): i for i, j in enumerate(xaxis)}
return sorted(vals[i.name] for i in self.xinfo
if i.name in vals and getattr(i, attr))
class StatsPlotSelectorTheme:
"theme for beads plot"
points: PlotAttrs = field(default_factory=lambda: PlotAttrs(
'#fdae6b', 'x', x='x', y='y', size=10, line_width=2))