Creates a visual representation of gramian angular field corresponding to the given poly(A) tail fragment (chunk).

The function uses a rainbow palette from grDevices, which makes the matrix more visually pleasing than greyscale (however this is just a visual sugar for human user, as the computer "sees" the data in greyscale (each of 2 dimensions as single-channel matrix).

Usage

plot_gaf(gaf_name, gaf_list, save_file = FALSE)

Arguments

gaf_name: character string. Name of the given read segment (chunk) for which the gaf is meant to be plotted. This is the name of the given gaf within the gaf_list produced by the create_gaf_list function.
gaf_list: A list of gaf matrices organized by the read ID_index.
save_file: logical [TRUE/FALSE]. If TRUE, the gaf plot 100x100 (pixels) would be saved in the current workng directory. If FALSE, the plot would be displayed only in the window. This parameter is set to FALSE by default.

Value

gramian angular field representing given fragment of nanopore read signal.

Details

IMPORTANT NOTE! Please keep in mind that the matrices produced by ninetails pipeline are originally two-dimensional arrays (GASF & GADF combined). Each of the dimensions are plotted alltogether (collapsed) as a single depiction. However, they can be splitted, but this requires additional processing steps. For the purpose of ONT signal classification, this combined GASF + GADF approach turned out to be the most suitable, thus the single-dimension extraction is currently not implemented within ninetails plotting functions (which does not mean it would not be).

User can control the size of the plot by defining the dimensions within the code chunk in R/RStudio. However, please keep in mind that the ninetails' default built-in model was trained on 100x100 gasfs.

Examples

if (FALSE) { # \dontrun{

example_gaf <- ninetails::plot_gaf(
 gaf_name = "5c2386e6-32e9-4e15-a5c7-2831f4750b2b_1",
 gaf_list = gl,
 save_file = TRUE)

print(example_gaf)

} # }