This function plots the collection of sequences as an image matrix.
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" )
The sequences as a DNAStringSet object.
The labels to be used for the sequence positions. Default: Sequence positions are labeled from 1 to the length of the sequences.
The x-axis tick frequency. Expects a positive integer less than the length of the sequences. Default is 5.
The y-axis tick frequency. Expects a positive integer less than number of sequences. Default is 100.
A vector of four colors used for the DNA bases A, C, G, and T (in that order).
Logical. Whether legend should be added to the plot. Default is TRUE.
A character vector of letters in the input sequences.
DNA_BASES, used for DNA sequences.
Specify the filename (with extension) for saving the plot to disk.
Specify the file type, namely PNG, JPEG, TIFF.
Specify the width for the plot. This depends on the length of sequences.
Specify the height for the plot. This depends on the number of sequences.
Specify the units in which the height and width are given.
Nothing returned to the R interpreter.
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)