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Draws tail range squiggle for given read from POD5 file.

Source: R/ninetails_plotting_functions.R
plot_tail_range_pod5.Rd

Creates segmented plot of raw or rescaled ONT RNA signal from Dorado basecalled POD5 files, focused on the poly(A) tail region with flanking sequences.

Usage

plot_tail_range_pod5(
  readname,
  dorado_summary,
  workspace,
  flank = 150,
  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 the POD5 files.

flank

Numeric. Number of positions to include on each side of the poly(A) region. Default is 150.

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 centered on tail range.

Details

The output plot includes the tail region (orange) and user-defined flanks of adapter (blue) and transcript body (black) regions. 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_tail_range_fast5 for the fast5 equivalent, plot_squiggle_pod5 for full signal plot

Examples

if (FALSE) { # \dontrun{

# Basic usage (no non-A overlay)
plot <- ninetails::plot_tail_range_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_tail_range_pod5(
  readname = "0e8e52dc-3a71-4c33-9a00-e1209ba4d2e9",
  dorado_summary = "dorado_summary.txt",
  workspace = "/path/to/pod5/",
  residue_data = "nonadenosine_residues.txt",
  nonA_flank = 250)

print(plot)

} # }