plt.xlabel('R2 for {}'.format(fitter1.shape), fontsize=cfg.fontsize)
plt.ylabel('R2 for {}'.format(fitter2.shape), fontsize=cfg.fontsize)
return fig
if __name__ == '__main__':
disable_all_warnings()
parser = get_common_parser()
parser.add_argument('--shape2', required=True, help='The shape to compare against', choices=allowed_shape_names())
parser.add_argument('--scaling2', help='The scaling used when fitting shape2. Default: none', choices=allowed_scaler_names())
parser.add_argument('--sigma_prior2', help='Prior to use for 1/sigma when fitting shape2. Default: None', choices=get_allowed_priors(is_sigma=True))
parser.add_argument('--priors2', help='The priors used for theta when fitting shape2. Default: None', choices=get_allowed_priors())
parser.add_argument('--filename', help='Where to save the figure. Default: results/comparison.png')
parser.add_argument('--show', help='Show figure and wait before exiting', action='store_true')
parser.add_argument('--ndiffs', type=int, default=5, help='Number of top diffs to show. Default=5.')
args = parser.parse_args()
data1, fitter1 = process_common_inputs(args)
data2 = get_data_from_args(args.dataset, args.pathway, args.from_age, args.scaling2, args.shuffle)
fitter2 = get_fitter_from_args(args.shape2, args.priors2, args.sigma_prior2)
fits1 = get_all_fits(data1,fitter1)
fits2 = get_all_fits(data2,fitter2)
print_diff_points(data1,fitter1,fits1, data2,fitter2,fits2, args.ndiffs)
fig = plot_comparison_scatter(data1,fitter1,fits1, data2,fitter2,fits2)
filename = args.filename
if filename is None:
ensure_dir(results_dir())
filename = join(results_dir(), 'shape_comparison.png')
save_figure(fig, filename)
fig = plot_series(series)
if filename is None:
ensure_dir(results_dir())
filename = join(results_dir(), 'fits.png')
print 'Saving figure to {}'.format(filename)
save_figure(fig, filename)
if b_show:
plt.show(block=True)
if __name__ == '__main__':
disable_all_warnings()
cfg.fontsize = 18
cfg.xtick_fontsize = 18
cfg.ytick_fontsize = 18
parser = get_common_parser(include_pathway=False)
parser.add_argument('-g', '--genes', default='HTR1A HTR1E')
parser.add_argument('-r', '--region', default='VFC')
group = parser.add_mutually_exclusive_group()
group.add_argument('--loo', help='Show LOO predictions', action='store_true')
group.add_argument('--nofit', help='Only show the data points', action='store_true')
parser.add_argument('--filename', help='Where to save the figure. Default: results/fit.png')
parser.add_argument('--show', help='Show figure and wait before exiting', action='store_true')
args = parser.parse_args()
data, fitter = process_common_inputs(args)
genes = args.genes.split()
if args.nofit:
fitter = None
series = data.get_several_series(genes,args.region)
fit_serveral_genes(series, fitter, args.loo, args.filename, args.show)
abort('--correlations_part cannot should not used with --html')
if args.onset and not is_sigmoid:
abort('--onset can only be used with sigmoid fits')
if args.change_dist and not is_sigmoid:
abort('--change_dist can only be used with sigmoid fits')
if args.onset and args.html == NOT_USED:
abort('--onset should only be used with --html')
if args.text and args.shape != 'spline':
abort('--text only supported for splines at the moment')
if (args.exons_layout or args.exons_same_scale or args.exons_plots_from_series) and args.html == NOT_USED:
abort('exons settings are relevant only when using --html')
if (args.exons_same_scale or args.plots_scaling is not 'none') and args.exons_plots_from_series:
abort('--exons_same_scale/--plots_scaling are relevant only when not using --exons_plots_from_series')
k_of_n = parse_k_of_n(args.part)
correlations_k_of_n = parse_k_of_n(args.correlations_part)
data, fitter = process_common_inputs(args)
fits = do_fits(data, fitter, k_of_n, args.correlations, correlations_k_of_n)
has_change_distributions = is_sigmoid
if has_change_distributions:
print 'Computing change distributions...'
add_change_distributions(data, fitter, fits)
if args.change_dist:
print 'Computing region pair timing measures...'
compute_dprime_measures_for_all_pairs(data, fitter, fits)
export_timing_info_for_all_fits(data, fitter, fits)
if args.html != NOT_USED:
if args.correlations:
correlations = {r: rfits[-1].correlations for r,rfits in iterate_region_fits(data, fits)}
else:
correlations = None
exons_layout = args.exons_layout and cfg.exon_level
