FeatureContribution

FeatureContribution#

class alphagenome.visualization.plot_components.FeatureContribution(feature_contributions, *, width=1.0, fig_height=3.0, feature_colormap=immutabledict({'PROTEIN_TERMINATION': '#52606d', 'START_LOST': '#94a3b0', 'STOP_LOST': '#d2dae2', 'ALPHAMISSENSE': '#4393c3', 'PHASTCONS_470_WAY': '#80dab4', 'CACTUS_241_WAY': '#379577', 'MAX_ABS_CAGE': '#868beb', 'MAX_ABS_PROCAP': '#c3c4f5', 'MAX_ABS_RNA_SEQ': '#2a2d78', 'MERGED_SPLICING': '#f3a380', 'MAX_ABS_POLYADENYLATION': '#555ac6', 'MAX_ABS_ATAC': '#f0e801', 'MAX_ABS_DNASE': '#c5be0f', 'MAX_ABS_CHIP_TF': '#f5b8f5', 'MAX_ABS_CHIP_HISTONE': '#df62df', 'MAX_ABS_CONTACT_MAPS': '#fbf68d'}), feature_order=('MAX_ABS_ATAC', 'MAX_ABS_CONTACT_MAPS', 'MAX_ABS_DNASE', 'MAX_ABS_CHIP_TF', 'MAX_ABS_CHIP_HISTONE', 'MAX_ABS_CAGE', 'MAX_ABS_PROCAP', 'MAX_ABS_RNA_SEQ', 'MAX_ABS_POLYADENYLATION', 'MERGED_SPLICING', 'ALPHAMISSENSE', 'START_LOST', 'STOP_LOST', 'PROTEIN_TERMINATION', 'PHASTCONS_470_WAY', 'CACTUS_241_WAY'), ylabel='', show_legend=False, max_y_ticks=3, default_color='#888888')[source]#

Stacked SHAP bar chart showing feature importance per variant.

Initializes the FeatureContribution component.

Parameters:

  • feature_contributions (AnnData) – AnnData with feature contribution scores shaped (n_variants, num_features). Must contain a 'variant' column in obs. When multiple variants share a genomic position, the variant with the maximum sum of feature contributions is plotted.

  • width (float (default: 1.0)) – Width of the bars.

  • fig_height (float (default: 3.0)) – Height of the panel in inches.

  • feature_colormap (Mapping[str, str] (default: immutabledict({'PROTEIN_TERMINATION': '#52606d', 'START_LOST': '#94a3b0', 'STOP_LOST': '#d2dae2', 'ALPHAMISSENSE': '#4393c3', 'PHASTCONS_470_WAY': '#80dab4', 'CACTUS_241_WAY': '#379577', 'MAX_ABS_CAGE': '#868beb', 'MAX_ABS_PROCAP': '#c3c4f5', 'MAX_ABS_RNA_SEQ': '#2a2d78', 'MERGED_SPLICING': '#f3a380', 'MAX_ABS_POLYADENYLATION': '#555ac6', 'MAX_ABS_ATAC': '#f0e801', 'MAX_ABS_DNASE': '#c5be0f', 'MAX_ABS_CHIP_TF': '#f5b8f5', 'MAX_ABS_CHIP_HISTONE': '#df62df', 'MAX_ABS_CONTACT_MAPS': '#fbf68d'}))) – Mapping from feature names to colors. Defaults to FEATURE_CONTRIBUTIONS_COLORMAP.

  • feature_order (Sequence[str] (default: ('MAX_ABS_ATAC', 'MAX_ABS_CONTACT_MAPS', 'MAX_ABS_DNASE', 'MAX_ABS_CHIP_TF', 'MAX_ABS_CHIP_HISTONE', 'MAX_ABS_CAGE', 'MAX_ABS_PROCAP', 'MAX_ABS_RNA_SEQ', 'MAX_ABS_POLYADENYLATION', 'MERGED_SPLICING', 'ALPHAMISSENSE', 'START_LOST', 'STOP_LOST', 'PROTEIN_TERMINATION', 'PHASTCONS_470_WAY', 'CACTUS_241_WAY'))) – Desired order of features in the plot. Defaults to FEATURE_CONTRIBUTIONS_ORDER.

  • ylabel (str (default: '')) – Y-axis label.

  • show_legend (bool (default: False)) – Whether to display a legend.

  • max_y_ticks (int | None (default: 3)) – Maximum number of Y-axis tick divisions (default: 3).

  • default_color (str (default: '#888888')) – Fallback color for features not in feature_colormap.

Raises:

ValueError – If 'variant' is not in feature_contributions.obs.

Methods

get_ax_height(axis_index)

Returns the height of the axis.

plot_ax(ax, axis_index, interval)

Plots the bar chart on the given axis.