smftools.plotting.pod5_plotting

POD5 signal plotting utilities for nanopore reads.

Functions

plot_read_current_traces(adata, read_ids[, ...])

Plot raw current signal from POD5 files for specified reads.

smftools.plotting.pod5_plotting.plot_read_current_traces(adata, read_ids, reference_start=None, reference_end=None, var_start=None, var_end=None, use_moves=True, figsize=(15, 4), title=None, pod5_dir=None, save_path=None)

Plot raw current signal from POD5 files for specified reads.

Parameters

adataanndata.AnnData

AnnData object with obs['fn'] or obs['pod5_origin'] (POD5 filenames) and uns['bam_paths'] (experiment-specific BAM file paths).

read_idslist of str

List of read IDs to plot.

reference_startint, optional

Start position in reference coordinates (0-based). If provided with reference_end, only plot signal for this genomic region.

reference_endint, optional

End position in reference coordinates (0-based, exclusive).

var_startint, optional

Start var index (0-based) into adata.var. The corresponding reference coordinate is looked up from adata.var["Original_var_names"] (if the adata was reindexed) or adata.var_names. Takes precedence over reference_start / reference_end when both are provided.

var_endint, optional

End var index (0-based, exclusive).

use_movesbool, default True

If True and move table (mv tag) is available, use it for precise signal-to-base mapping. If False or mv tag unavailable, use proportional estimation.

figsizetuple, default (15, 4)

Figure size (width, height) in inches.

titlestr, optional

Plot title. If None, uses read ID.

pod5_dirstr or Path, optional

Directory containing POD5 files. When provided, the basename from obs['fn'] / obs['pod5_origin'] is joined with this directory to form the absolute path.

save_pathstr or Path, optional

If provided, save the figure to this path as PNG.

Returns

figmatplotlib.figure.Figure

The created figure object.

Notes

Requires POD5 files to be accessible at the paths stored in obs['fn'] or obs['pod5_origin']. For precise signal mapping, requires BAM files with move tables (mv tag) generated using dorado's --emit-moves flag.

Examples

>>> plot_read_current_traces(adata, ["read_001", "read_002"],
...                          reference_start=1000, reference_end=1500)
>>> # Or use var indices to plot signal for a span of adata columns:
>>> plot_read_current_traces(adata, ["read_001"], var_start=0, var_end=100)