| |
| |
| import numpy as np |
| import pandas as pd |
| import matplotlib.pyplot as plt |
| import matplotlib.font_manager |
| import matplotlib.ticker as mticker |
| from matplotlib import rc |
| plt.rcParams['text.usetex'] = True |
| plt.rcParams["font.family"] = 'Optima' |
| plt.rcParams["font.size"] = 20 |
| plt.rc('axes', unicode_minus=False) |
| plt.tight_layout() |
|
|
|
|
| def make_plots(log_scale: bool): |
| aic_fig, aic_ax = plt.subplots(figsize=[8,6]) |
| xax_lab = 'Number of parameters' |
| |
| def add_to_plots(mixture_type, |
| label, |
| color, |
| linestyle = '-', |
| marker = 'o'): |
| |
| sub_df = df[ df['model_type'] == mixture_type ] |
| sub_df = sub_df.sort_values(by='parameters') |
| assert len(sub_df) > 0 |
| |
| |
| aic_ax.plot( sub_df['parameters'], |
| sub_df['aic_gain'], |
| marker = marker, |
| linestyle = linestyle, |
| color = color, |
| label = label, |
| linewidth = 3.5, |
| markersize = 10) |
| |
| del sub_df, label |
| |
| add_to_plots(mixture_type = 'pairhmm_domain_mix', |
| label = 'Mixture of domain classes', |
| color = 'tab:purple') |
| |
| add_to_plots(mixture_type = 'pairhmm_fragment_mix', |
| label = 'Mixture of fragment classes', |
| color = 'tab:green') |
| |
| add_to_plots(mixture_type = 'pairhmm_site_mix', |
| label = 'Mixture of site classes', |
| color = 'tab:orange') |
| |
| aic_ax.grid() |
| aic_ax.legend() |
| aic_ax.set_xlabel(xax_lab) |
| aic_ax.set_ylabel('$\Delta$AIC (×$10^7$)') |
| new_y_tick_labels = [f"{x:.1e}".split("e")[0] for x in aic_ax.get_yticks()] |
| aic_ax.set_yticklabels( new_y_tick_labels ) |
| del new_y_tick_labels |
| |
| if log_scale: |
| aic_ax.set_xscale('log') |
| |
| aic_fig.savefig(f'AIC_parameters_log_{log_scale}.pdf', |
| bbox_inches="tight") |
|
|
|
|
| def read_file(file): |
| df = pd.read_csv(file, sep='\t', index_col=0) |
| sub_df = df[ (df['dataset'] == 'data1') & |
| (df['sub_model'] == 'f81') & |
| (df['indel_model'] == 'tkf92') ] |
| sub_df = sub_df[['sub_model', |
| 'indel_model', |
| 'model_type', |
| 'parameters', |
| 'aic', |
| 'bic']] |
| sub_df = sub_df.sort_values(by='parameters') |
| |
| ref = sub_df[ sub_df['model_type']=='pairhmm_reference' ] |
| sub_df['aic_gain'] = ref['aic'].item() - sub_df['aic'] |
| sub_df['bic_gain'] = ref['bic'].item() - sub_df['bic'] |
| |
| sub_df = sub_df.drop( ['aic','bic'], axis=1 ) |
| sub_df = sub_df[ sub_df['model_type'] !='pairhmm_reference' ] |
| return sub_df |
|
|
|
|
| if __name__ == '__main__': |
| df = read_file('hierarchical_mixture_models_train_set_loglikes.tsv') |
| make_plots(log_scale = True) |
|
|
