Plotting: pl

Plotting: `pl`#

Figure-rendering functions used by the CLI pipeline stages and available for direct use in notebooks/scripts.

`smftools.plotting.autocorrelation_plotting`
`smftools.plotting.chimeric_plotting`
`smftools.plotting.classifiers`
`smftools.plotting.general_plotting`
`smftools.plotting.hmm_plotting`
`smftools.plotting.latent_plotting`
`smftools.plotting.plotting_utils`
`smftools.plotting.pod5_plotting`	POD5 signal plotting utilities for nanopore reads.
`smftools.plotting.position_stats`
`smftools.plotting.preprocess_plotting`
`smftools.plotting.qc_plotting`
`smftools.plotting.spatial_plotting`
`smftools.plotting.umi_plotting`	Plotting utilities for UMI bipartite graph analysis.
`smftools.plotting.variant_plotting`

qc_plotting includes plot_read_qc_histograms (read length/quality/mapping QC, used by smftools preprocess) and plot_reference_barcode_chimera_rate (the deaminase PCR-chimera-rate heatmap written by smftools raw).