def main():
parser = argparse.ArgumentParser(
description='LOL HI THERE',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--template', default='seaborn')
parser.add_argument('--max-y')
parser.add_argument('--score-type',
required=True,
choices=('mutrel', 'mutphi', 'mutdistl1', 'mutdistl2'))
parser.add_argument('--baseline')
parser.add_argument('results_fn')
parser.add_argument('single_method')
parser.add_argument('plot_fn')
args = parser.parse_args()
results, methods = plotter.load_results(args.results_fn)
plot_type = 'box'
plotter.munge(results, methods, args.baseline, args.score_type, plot_type)
for key in ('K', 'S'):
results = plotter.augment(results, key)
boxes = make_boxes(results, methods, args.single_method)
figs = {
f'scores_{args.single_method}_vs_others':
plotter.make_fig(
boxes,
args.template,
plotter.make_score_ytitle(args.score_type, args.plot_fn),
args.max_y,
log_y_axis=False,
layout_options={},
),
}
plotter.write_figs(figs, args.plot_fn)
def main():
parser = argparse.ArgumentParser(
description='LOL HI THERE',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--template', default='seaborn')
parser.add_argument('--max-y')
parser.add_argument('--score-type',
required=True,
choices=('mutrel', 'mutphi', 'mutdistl1', 'mutdistl2'))
parser.add_argument('--baseline')
parser.add_argument('results_fn')
parser.add_argument('method')
parser.add_argument('plot_fn')
args = parser.parse_args()
results, methods = plotter.load_results(args.results_fn)
plot_type = 'box'
plotter.munge(results, methods, args.baseline)
for key in ('K', 'S'):
results = plotter.augment(results, key)
score_traces = make_score_traces(results, args.method)
completion_traces = make_completion_traces(results, args.method)
figs = {
f'scores_{args.method}':
plotter.make_fig(
score_traces,
args.template,
plotter.make_score_ytitle(args.score_type, args.plot_fn),
args.max_y,
log_y_axis=False,
layout_options={
'boxmode': 'group',
'violinmode': 'overlay',
'violingap': 0.0,
'violingroupgap': 0.0,
},
),
f'completion_{args.method}':
plotter.make_fig(
completion_traces,
args.template,
'Failure rate',
100,
log_y_axis=False,
layout_options={
'barmode': 'group',
},
),
}
plotter.write_figs(figs, args.plot_fn)
def main():
parser = argparse.ArgumentParser(
description='LOL HI THERE',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--template', default='seaborn')
parser.add_argument('--score-type',
required=True,
choices=('mutphi', 'mutdistl1', 'mutdistl2'))
parser.add_argument('--hide-methods')
parser.add_argument('--baseline')
parser.add_argument('results_fn')
parser.add_argument('plot_fn')
args = parser.parse_args()
results, methods = plotter.load_results(args.results_fn)
plotter.munge(results, methods, args.baseline)
methods = set(methods)
methods -= set(args.hide_methods.split(','))
method_colours = plotter.choose_method_colours(methods)
figs = {
'scores':
_plot_scores(
results,
methods - set(('mle_unconstrained', )),
method_colours,
),
}
export_dims = {
'scores': (600, 500),
}
for M in methods:
if M == 'mle_unconstrained':
continue
name = f'{M}_vs_others'
figs[name] = _plot_single_vs_others(
results,
M,
methods, # - set(('mle_unconstrained',)),
method_colours,
)
export_dims[name] = (600, 485)
for F in figs.values():
if 'layout' not in F:
F['layout'] = {}
F['layout']['template'] = args.template
plotter.write_figs(figs, args.plot_fn, export_dims)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--mutrels', dest='mutrel_fn')
parser.add_argument('entropy_fn')
parser.add_argument('plot_fn')
args = parser.parse_args()
results = pd.read_csv(args.entropy_fn)
if args.mutrel_fn is not None:
mrel_meth, mrel_fn = args.mutrel_fn.split('=', 1)
mrel = pd.read_csv(mrel_fn)
mrel = mrel.filter(('runid', mrel_meth))
mrel = mrel.rename(columns={mrel_meth: 'mutrel'})
assert MISSING not in mrel['mutrel']
assert set(results['runid']) == set(mrel['runid'])
results = pd.merge(results, mrel, on='runid', how='outer')
results['H_trees_pairtree_3_minus_H_trees_truth'] = results[
'H_trees_pairtree_3'] - results['H_trees_truth']
results, unique_keys = partition(results, ('K', 'S'))
figs = {}
export_dims = {}
for name, title, shared_y, log_y in (
('true_trees', 'Trees consistent with<br>true lineage frequencies',
False, True),
('jsd_parents_mean',
'Parent JSD between tree parents<br>and Pairtree parents (bits)',
True, False),
('H_trees_pairtree_3_minus_H_trees_truth',
'Difference in tree entropy distribution<br>between Pairtree and truth (bits)',
False, False),
('mutrel', 'Pairwise relation error (bits)', True, False),
):
figs[name] = plot(results, unique_keys, name, title, shared_y, log_y)
export_dims[name] = (700, 400)
figs['true_trees'].update_yaxes(rangemode='tozero')
#for idx, K in enumerate(unique_keys['K']):
# logmax = np.log10(np.max(results['true_trees'][results['K'] == K]))
# figs['true_trees'].update_yaxes(range = [-0.1, np.ceil(logmax)], row=1, col=idx+1)
plotter.write_figs(figs, args.plot_fn, export_dims)
def main():
parser = argparse.ArgumentParser(
description='LOL HI THERE',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--S-threshold', type=int)
parser.add_argument('--template', default='seaborn')
parser.add_argument('--max-y')
parser.add_argument('--score-type',
required=True,
choices=('mutrel', 'mutphi', 'mutdistl1', 'mutdistl2',
'cputime', 'walltime'))
parser.add_argument('--baseline')
parser.add_argument('--bandwidth', type=float)
parser.add_argument('--plot-type',
choices=('box', 'violin'),
default='box')
parser.add_argument('--log-y-axis', action='store_true')
parser.add_argument('--hide-method', nargs='+')
parser.add_argument('results_fn')
parser.add_argument('plot_fn')
args = parser.parse_args()
results, methods = plotter.load_results(args.results_fn)
if args.hide_method is not None:
methods = [M for M in methods if M not in args.hide_method]
plotter.munge(results, methods, args.baseline, args.score_type,
args.plot_type)
sides = {
'lte': 'negative',
'gt': 'positive',
}
names = {
'lte': '1 or 3 tissue samples',
'gt': '10, 30, or 100 tissue samples',
}
colours = {
'lte': 'rgb(55,126,184)',
'gt': 'rgb(152,78,163)',
}
score_traces = []
completion_bar_traces = []
completion_pie_figs = []
if args.S_threshold is not None:
results = plotter.augment(results, 'S')
parted_by_S = plotter.partition(results, methods, key='S')
parted_by_thresh = plotter.partition_by_threshold(
parted_by_S, args.S_threshold)
for group in parted_by_thresh.keys():
vals = parted_by_thresh[group]
if len(vals) == 0:
continue
methods = [M for M in vals.keys()]
scores = {M: vals[M]['scores'] for M in methods}
complete = {M: vals[M]['complete'] for M in methods}
total = {M: vals[M]['total'] for M in methods}
X, Y = plotter.make_points_for_methods(scores)
if args.plot_type == 'box':
score_trace = plotter.make_box_trace(X,
Y,
group=group,
name=names[group],
colour=colours[group])
elif args.plot_type == 'violin':
score_trace = plotter.make_violin_trace(
X,
Y,
side=sides[group],
group=group,
name=names[group],
bandwidth=args.bandwidth,
colour=colours[group])
else:
raise Exception('Unknown plot type %s' % args.plot_type)
score_traces.append(score_trace)
completion_bar_traces.append(
plotter.make_bar_trace(methods,
complete,
total,
name=names[group]))
completion_pie_figs.append(
plotter.make_pie_fig(methods,
complete,
total,
name=names[group]))
else:
scores = {M: np.array(results[M]) for M in methods}
total = {M: len(scores[M]) for M in methods}
complete = {M: np.sum(scores[M] != MISSING) for M in methods}
X, Y = plotter.make_points_for_methods(scores)
if args.plot_type == 'box':
score_trace = plotter.make_box_trace(X, Y, colour=colours['lte'])
elif args.plot_type == 'violin':
score_trace = plotter.make_violin_trace(X,
Y,
side='both',
bandwidth=args.bandwidth)
score_traces.append(score_trace)
completion_bar_traces.append(
plotter.make_bar_trace(methods, complete, total))
completion_pie_figs.append(
plotter.make_pie_fig(methods, complete, total))
figs = [
plotter.make_fig(
score_traces,
args.template,
plotter.make_score_ytitle(args.score_type, args.plot_fn),
args.max_y,
log_y_axis=args.log_y_axis,
layout_options={
'boxmode': 'group',
'violinmode': 'overlay',
'violingap': 0.0,
'violingroupgap': 0.0,
},
),
plotter.make_fig(
completion_bar_traces,
args.template,
'Proportion of failed runs',
max_y=None,
layout_options={'barmode': 'group'},
),
]
figs += completion_pie_figs
plotter.write_figs(figs, args.plot_fn)
def main():
parser = argparse.ArgumentParser(
description='LOL HI THERE',
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument('--template', default='seaborn')
parser.add_argument('--score-type', required=True, choices=('mutrel', 'mutphi', 'mutdistl1', 'mutdistl2', 'cputime', 'walltime'))
parser.add_argument('--baseline')
parser.add_argument('--hide-methods', default='')
parser.add_argument('results_fn')
parser.add_argument('plot_fn')
args = parser.parse_args()
_make_axis_titles()
results, methods = plotter.load_results(args.results_fn)
plotter.munge(results, methods, args.baseline)
for key in ('K', 'S'):
results = plotter.augment(results, key)
methods = set(methods)
methods -= set(args.hide_methods.split(','))
method_colours = plotter.choose_method_colours(methods)
figs = {
'scores': _plot_scores(
results,
methods - set(('mle_unconstrained',)),
method_colours,
args.score_type
),
'success_rate': _plot_success_rates(
results,
methods - set(('mle_unconstrained', 'pwgs_supervars', 'lichee', 'pairtree_clustrel')),
method_colours,
(3, 10),
(1, 3, 10),
),
'S_comparison': _plot_S_comparison(
results,
methods - set(('mle_unconstrained', 'citup', 'pastri')),
method_colours,
(3, 10, 30),
(1, 3, 10, 30, 100),
args.score_type
),
}
export_dims = {
'success_rate': (400, 485),
}
export_dims['scores'] = (700, 850)
export_dims['S_comparison'] = (500, 485)
for M in plotter.sort_methods(methods):
if M == 'mle_unconstrained':
continue
name = f'{M}_vs_others'
figs[name] = _plot_single_vs_others(
results,
M,
methods,# - set(('mle_unconstrained',)),
method_colours,
args.score_type
)
export_dims[name] = (600, 485)
for F in figs.values():
if 'layout' not in F:
F['layout'] = {}
F['layout']['template'] = args.template
plotter.write_figs(figs, args.plot_fn, export_dims)