smftools.plotting.preprocess_plotting

smftools.plotting.preprocess_plotting#

Functions

plot_read_span_quality_clustermaps(adata[, ...])

Plot read-span mask and base quality clustermaps side by side.
smftools.plotting.preprocess_plotting.plot_read_span_quality_clustermaps(adata, sample_col='Sample_Names', reference_col='Reference_strand', quality_layer='base_quality_scores', read_span_layer='read_span_mask', quality_cmap='viridis', read_span_color='#2ca25f', sort_method='hierarchical', pca_n_components=20, pca_sort_component=0, max_nan_fraction=None, min_quality=None, min_length=None, min_mapped_length_to_reference_length_ratio=None, demux_types=('single', 'double', 'already'), max_reads=None, xtick_step=None, xtick_rotation=90, xtick_fontsize=9, show_position_axis=False, position_axis_tick_target=25, save_path=None, n_jobs=1, index_col_suffix=None)#

Plot read-span mask and base quality clustermaps side by side.

Clustering is performed using the base-quality layer ordering, which is then applied to the read-span mask to keep the two panels aligned.

Parameters:

  • adata -- AnnData with read-span and base-quality layers.

  • sample_col (str (default: 'Sample_Names')) -- Column in adata.obs that identifies samples.

  • reference_col (str (default: 'Reference_strand')) -- Column in adata.obs that identifies references.

  • quality_layer (str (default: 'base_quality_scores')) -- Layer name containing base-quality scores.

  • read_span_layer (str (default: 'read_span_mask')) -- Layer name containing read-span masks.

  • quality_cmap (str (default: 'viridis')) -- Colormap for base-quality scores.

  • read_span_color (str (default: '#2ca25f')) -- Color for read-span mask (1-values); 0-values are white.

  • sort_method (str (default: 'hierarchical')) -- Row ordering strategy ("pca" or "hierarchical").

  • pca_n_components (int | None (default: 20)) -- Number of PCA components to compute for ordering. If None, uses min(n_reads, n_positions).

  • pca_sort_component (int (default: 0)) -- Zero-based PCA component index to sort by (ascending).

  • max_nan_fraction (float | None (default: None)) -- Optional maximum fraction of NaNs allowed per position; positions above this threshold are excluded.

  • min_quality (float | None (default: None)) -- Optional minimum read quality filter.

  • min_length (int | None (default: None)) -- Optional minimum mapped length filter.

  • min_mapped_length_to_reference_length_ratio (float | None (default: None)) -- Optional min length ratio filter.

  • demux_types (Sequence[str] (default: ('single', 'double', 'already'))) -- Allowed demux_type values, if present in adata.obs.

  • max_reads (int | None (default: None)) -- Optional maximum number of reads to plot per sample/reference.

  • xtick_step (int | None (default: None)) -- Spacing between x-axis tick labels (None = no labels).

  • xtick_rotation (int (default: 90)) -- Rotation for x-axis tick labels.

  • xtick_fontsize (int (default: 9)) -- Font size for x-axis tick labels.

  • show_position_axis (bool (default: False)) -- Whether to draw a position axis with tick labels.

  • position_axis_tick_target (int (default: 25)) -- Approximate number of ticks to show when auto-sizing.

  • save_path (str | Path | None (default: None)) -- Optional output directory for saving plots.

  • n_jobs (int (default: 1)) -- Number of parallel worker processes. -1 uses all available CPUs. Parallelism is only applied when save_path is set (interactive display is always serial).

  • index_col_suffix (str | None (default: None)) -- If set, use adata.var[f"{ref}_{index_col_suffix}"] for tick labels and column order instead of var_names (e.g. "reindexed"), matching the HMM/spatial clustermaps.

Return type:

List[Dict[str, Any]]

Returns:

List of dictionaries with per-plot metadata and output paths.