fig = plt.figure() plt.scatter(scores1, scores2, alpha=0.5) plt.plot([-1, 1], [-1, 1],'k--') plt.xlim(-1,1) plt.ylim(-1,1) ttl1 = r'Comparison of scores using {} vs. {}'.format(fitter1.shape,fitter2.shape) ttl2 = r'{}, {}'.format(data1.name, data1.pathway) plt.title('\n'.join([ttl1, ttl2]), fontsize=cfg.fontsize) 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)
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)
if b_show: plt.show(block=True) def do_gene_fits(data, gene, fitter, filename, b_show): fig = plot_gene(data,gene) if filename is None: ensure_dir(results_dir()) filename = join(results_dir(), 'fit.png') print 'Saving figure to {}'.format(filename) save_figure(fig, filename) if b_show: plt.show(block=True) if __name__ == '__main__': disable_all_warnings() parser = get_common_parser(include_pathway=False) parser.add_argument('-g', '--gene', default='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) if args.nofit: fitter = None if args.region == 'all': do_gene_fits(data, args.gene, fitter,args.filename,args.show) else: series = data.get_one_series(args.gene,args.region)