proteobench.plotting.plot_denovo module#

Module for plotting results of de novo models

class proteobench.plotting.plot_denovo.PlotDataPoint[source]#

Bases: object

Class for plotting data points.

static get_modification_scores(mod_dict, mod_labels)[source]#

static plot_metric(benchmark_metrics_df: DataFrame, level: str = 'precision', evaluation_type: str = 'mass', software_colors: Dict[str, str] = {'AdaNovo': '#8b26ff', 'Casanovo': '#8bc6fd', 'DeepNovo': '#108E2E', 'PEAKS': '#f032e6', 'PepNet': '#F89008', 'Pi-HelixNovo': '#E43924', 'Pi-PrimeNovo': '#663200'}, mapping: Dict[str, int] = {'new': 20, 'old': 10}, highlight_color: str = '#d30067', label: str = 'None') → Figure[source]#

plot_ptm_overview(benchmark_metrics_df: DataFrame, mod_labels: List[str], software_colors: Dict[str, str] = {'AdaNovo': '#8b26ff', 'Casanovo': '#8bc6fd', 'DeepNovo': '#108E2E', 'PEAKS': '#f032e6', 'PepNet': '#F89008', 'Pi-HelixNovo': '#E43924', 'Pi-PrimeNovo': '#663200'})[source]#

plot_ptm_specific(benchmark_metrics_df, mod_label, software_colors: Dict[str, str] = {'AdaNovo': '#8b26ff', 'Casanovo': '#8bc6fd', 'DeepNovo': '#108E2E', 'PEAKS': '#f032e6', 'PepNet': '#F89008', 'Pi-HelixNovo': '#E43924', 'Pi-PrimeNovo': '#663200'})[source]#

plot_species_overview(benchmark_metrics_df, evaluation_type='mass', software_colors={'AdaNovo': '#8b26ff', 'Casanovo': '#8bc6fd', 'DeepNovo': '#108E2E', 'PEAKS': '#f032e6', 'PepNet': '#F89008', 'Pi-HelixNovo': '#E43924', 'Pi-PrimeNovo': '#663200', 'test': 'black'})[source]#

plot_species_specific()[source]#

plot_spectrum_feature(benchmark_metrics_df, feature, evaluation_type='mass', software_colors={'AdaNovo': '#8b26ff', 'Casanovo': '#8bc6fd', 'DeepNovo': '#108E2E', 'PEAKS': '#f032e6', 'PepNet': '#F89008', 'Pi-HelixNovo': '#E43924', 'Pi-PrimeNovo': '#663200', 'test': 'black'})[source]#

proteobench.plotting.plot_denovo.flatten_results_column(df)[source]#