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Draws an entire squiggle for given read from POD5 file.

Source: R/ninetails_plotting_functions.R
plot_squiggle_pod5.Rd

Creates segmented plot of raw or rescaled ONT RNA signal from Dorado basecalled POD5 files. A standalone function; depends solely on Dorado summary output and POD5 files.

Usage

plot_squiggle_pod5(
  readname,
  dorado_summary,
  workspace,
  rescale = FALSE,
  residue_data = NULL,
  nonA_flank = 250
)

Arguments

readname

Character string. Name of the given read (read_id) within the analyzed dataset.

dorado_summary

Character string or data frame. Either the full path to the Dorado summary file (.txt), or a pre-loaded data frame containing at minimum the columns: read_id, poly_tail_start, poly_tail_end, filename.

workspace

Character string. Full path of the directory containing POD5 files.

rescale

Logical [TRUE/FALSE]. If TRUE, the signal will be rescaled to picoamps (pA) per second (s). If FALSE, raw signal per position will be plotted. Default is FALSE.

residue_data

Character string, data frame, or NULL. Either the full path to the nonadenosine_residues output file, or a pre-loaded data frame. Required columns: read_id (or readname), prediction (C/G/U), est_nonA_pos, polya_length. If NULL (default), no overlay is drawn.

nonA_flank

Numeric. Number of raw signal positions to highlight on each side of the estimated non-A center. Default 250, matching the approximate extent of the 100-point interpolated chunk (~500 raw positions).

Value

ggplot2 object with squiggle plot depicting nanopore read signal.

Details

The output plot includes an entire squiggle corresponding to the given ONT read. Vertical lines mark the 5' (red) and 3' (navy blue) termini of polyA tail according to the Dorado poly(A) estimation. In order to maintain readability of the graph (and to avoid plotting high cliffs - e.g. jets of the signal caused by a sudden surge of current in the sensor) the signal is winsorized.

When residue_data is provided, semi-transparent rectangles highlight estimated non-adenosine residue positions within the poly(A) tail. Each rectangle spans +/- nonA_flank raw signal positions around the estimated modification center, matching the approximate extent of the 100-point interpolated chunk analyzed by the CNN.

See also

plot_squiggle_fast5 for the fast5 equivalent, plot_tail_range_pod5 for zoomed tail region plot

Examples

if (FALSE) { # \dontrun{

# Basic usage (no non-A overlay)
plot <- ninetails::plot_squiggle_pod5(
  readname = "0e8e52dc-3a71-4c33-9a00-e1209ba4d2e9",
  dorado_summary = system.file('extdata', 'test_data', 'pod5_DRS',
                               'aligned_summary.txt',
                               package = 'ninetails'),
  workspace = system.file('extdata', 'test_data', 'pod5_DRS',
                          package = 'ninetails'),
  rescale = FALSE)

# With non-A overlay
plot <- ninetails::plot_squiggle_pod5(
  readname = "0e8e52dc-3a71-4c33-9a00-e1209ba4d2e9",
  dorado_summary = "dorado_summary.txt",
  workspace = "/path/to/pod5/",
  residue_data = "nonadenosine_residues.txt")

print(plot)

} # }