viz_seqs_acgt_mat: Visualize raw DNA sequences as an image

In snikumbh/seqArchR: Identify Different Architectures of Sequence Elements

Visualize raw DNA sequences as an image

Description

This function plots the collection of sequences as an image matrix.

Usage

viz_seqs_acgt_mat(
  seqs,
  pos_lab = NULL,
  xt_freq = min(length(pos_lab), 5),
  yt_freq = min(length(seqs), 100),
  use_col = c("darkgreen", "blue", "orange", "red"),
  add_legend = TRUE,
  use_legend = Biostrings::DNA_BASES,
  save_fname = NULL,
  file_type = "PNG",
  f_width = 450,
  f_height = 900,
  f_units = "px"
)

Arguments

seqs	The sequences as a DNAStringSet object.
pos_lab	The labels to be used for the sequence positions. Default: Sequence positions are labeled from 1 to the length of the sequences.
xt_freq	The x-axis tick frequency. Expects a positive integer less than the length of the sequences. Default is 5.
yt_freq	The y-axis tick frequency. Expects a positive integer less than number of sequences. Default is 100.
use_col	A vector of four colors used for the DNA bases A, C, G, and T (in that order).
add_legend	Logical. Whether legend should be added to the plot. Default is TRUE.
use_legend	A character vector of letters in the input sequences. Default is DNA_BASES, used for DNA sequences.
save_fname	Specify the filename (with extension) for saving the plot to disk.
file_type	Specify the file type, namely PNG, JPEG, TIFF.
f_width	Specify the width for the plot. This depends on the length of sequences.
f_height	Specify the height for the plot. This depends on the number of sequences.
f_units	Specify the units in which the height and width are given.

Value

Nothing returned to the R interpreter.

See Also

Other visualization functions: viz_bas_vec(), viz_pwm()

Examples

res <- readRDS(system.file("extdata", "example_seqArchRresult.rds",
         package = "seqArchR", mustWork = TRUE))

# Image matrix of sequences in the input order
viz_seqs_acgt_mat(seqs = seqs_str(res))

# Image matrix of sequences ordered by the clustering from seqArchR
use_seqs <- seqs_str(res, iter = NULL, cl = NULL, ord = TRUE)
viz_seqs_acgt_mat(seqs = use_seqs)

# Image matrix of sequences belonging to a single cluster
use_seqs <- seqs_str(res, iter = 2, cl = 2)
viz_seqs_acgt_mat(seqs = use_seqs)

snikumbh/seqArchR documentation built on March 11, 2024, 7:06 p.m.