Description Usage Arguments Value See Also Examples
View source: R/viz_matrix_of_acgt_image.R
This function plots the collection of sequences as an image matrix.
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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 or. |
col |
A vector of four colors used for the DNA bases A, C, G, and T (in that order). |
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. |
Nothing returned to the R interpreter.
Other visualization functions:
plot_ggheatmap()
,
plot_ggseqlogo()
,
viz_bas_vec_heatmap_seqlogo()
1 2 3 4 5 6 7 8 9 10 11 12 13 | res <- readRDS(system.file("extdata", "example_archRresult.rds",
package = "archR", mustWork = TRUE))
# Image matrix of sequences in the input order
viz_seqs_acgt_mat_from_seqs(seqs = seqs_str(res))
# Image matrix of sequences ordered by the clustering from archR
use_seqs <- seqs_str(res, iter = NULL, cl = NULL, ord = TRUE)
viz_seqs_acgt_mat_from_seqs(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_from_seqs(seqs = use_seqs)
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