smftools.plotting.position_stats

smftools.plotting.position_stats#

Functions

plot_bar_relative_risk(results_dict[, ...])

Plot log2(Relative Risk) as a bar plot across genomic positions for each group within each reference.

plot_positionwise_matrix(adata[, key, ...])

Plots positionwise matrices stored in adata.uns[key], with an optional line plot for specified row(s) or column(s), and highlights them on the heatmap.

plot_positionwise_matrix_grid(adata, key[, ...])

Plot a grid of positionwise matrices grouped by metadata.

plot_volcano_relative_risk(results_dict[, ...])

Plot volcano-style log2(Relative Risk) vs Genomic Position for each group within each reference.
smftools.plotting.position_stats.plot_volcano_relative_risk(results_dict, save_path=None, highlight_regions=None, highlight_color='lightgray', highlight_alpha=0.3, xlim=None, ylim=None)#

Plot volcano-style log2(Relative Risk) vs Genomic Position for each group within each reference.

Parameters:

  • results_dict (dict) -- Output from calculate_relative_risk_by_group. Format: dict[ref][group_label] = (results_df, sig_df)

  • save_path (str) -- Directory to save plots.

  • highlight_regions (list) -- List of (start, end) tuples for shaded regions.

  • highlight_color (str) -- Color for highlighted regions.

  • highlight_alpha (float) -- Alpha for highlighted region.

  • xlim (tuple) -- Optional x-axis limit.

  • ylim (tuple) -- Optional y-axis limit.

smftools.plotting.position_stats.plot_bar_relative_risk(results_dict, sort_by_position=True, xlim=None, ylim=None, save_path=None, highlight_regions=None, highlight_color='lightgray', highlight_alpha=0.3)#

Plot log2(Relative Risk) as a bar plot across genomic positions for each group within each reference.

Parameters:

  • results_dict (dict) -- Output from calculate_relative_risk_by_group.

  • sort_by_position (bool) -- Whether to sort bars left-to-right by genomic coordinate.

  • xlim (tuple) -- Axis limits.

  • ylim (tuple) -- Axis limits.

  • save_path (str or None) -- Directory to save plots.

  • highlight_regions (list of tuple) -- List of (start, end) genomic regions to shade.

  • highlight_color (str) -- Color of shaded region.

  • highlight_alpha (float) -- Transparency of shaded region.

smftools.plotting.position_stats.plot_positionwise_matrix(adata, key='positionwise_result', log_transform=False, log_base='log1p', triangle='full', cmap='vlag', figsize=(12, 10), vmin=None, vmax=None, xtick_step=10, ytick_step=10, save_path=None, highlight_position=None, highlight_axis='row', annotate_points=False)#

Plots positionwise matrices stored in adata.uns[key], with an optional line plot for specified row(s) or column(s), and highlights them on the heatmap.

smftools.plotting.position_stats.plot_positionwise_matrix_grid(adata, key, outer_keys=['Reference_strand', 'activity_status'], inner_keys=['Promoter_Open', 'Enhancer_Open'], log_transform=None, vmin=None, vmax=None, cmap='vlag', save_path=None, figsize=(10, 10), xtick_step=10, ytick_step=10, parallel=False, max_threads=None)#

Plot a grid of positionwise matrices grouped by metadata.

Parameters:

  • adata -- AnnData containing matrices in adata.uns.

  • key -- Key for positionwise matrices.

  • outer_keys (default: ['Reference_strand', 'activity_status']) -- Keys for outer grouping.

  • inner_keys (default: ['Promoter_Open', 'Enhancer_Open']) -- Keys for inner grouping.

  • log_transform (default: None) -- Optional log transform (log2 or log1p).

  • vmin (default: None) -- Minimum color scale value.

  • vmax (default: None) -- Maximum color scale value.

  • cmap (default: 'vlag') -- Matplotlib colormap.

  • save_path (default: None) -- Optional path to save plots.

  • figsize (default: (10, 10)) -- Figure size.

  • xtick_step (default: 10) -- X-axis tick step.

  • ytick_step (default: 10) -- Y-axis tick step.

  • parallel (default: False) -- Whether to plot in parallel.

  • max_threads (default: None) -- Max thread count for parallel plotting.