plot_ggseqlogo_of_seqs: Plot sequence logo of a collection of sequences
In snikumbh/archR: Identify Different Architectures of Sequence Elements

Description Usage Arguments Value See Also Examples

A wrapper to ggseqlogo plotting. Given a collection of sequences, this function plots the sequence logo.

plot_ggseqlogo_of_seqs(
  seqs,
  pos_lab = NULL,
  xt_freq = 5,
  method = "bits",
  title = NULL,
  bits_yax = "full",
  fixed_coord = FALSE
)

`seqs`	Collection of sequences as a `DNAStringSet` object.
`pos_lab`	Labels for sequence positions, should be of same length as that of the sequences. Default value is NULL, when the positions are labeled from 1 to the length of the sequences.
`xt_freq`	Specify the frequency of the x-axis ticks.
`method`	Specify either 'bits' for information content or 'prob' for probability.
`title`	The title for the plot. Deafult is NULL.
`bits_yax`	Specify 'full' if the information content y-axis limits should be 0-2 or 'auto' for a suitable limit. The 'auto' setting adjusts the y-axis limits according to the maximum information content of the sequence logo. Default is 'full'.
`fixed_coord`	Specify TRUE if the aspect ratio of the plot should be fixed, FALSE otherwise. Default is TRUE. When 'method' argument is set to 'bits', ratio is 4, when 'prob', ratio is 6.

A sequence logo plot of the given DNA sequences.

plot_arch_for_clusters for obtaining multiple sequence logo plots as a list.

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

# Default, using information content on y-axis
pl <- plot_ggseqlogo_of_seqs(seqs = seqs_str(res, iter=1, cl=3),
                             pos_lab = seq_len(100), title = NULL,
                             fixed_coord = TRUE)
pl

# Using probability instead of information content
pl <- plot_ggseqlogo_of_seqs(seqs = seqs_str(res, iter=1, cl=3),
                             pos_lab = seq_len(100), title = "",
                             method = "prob", fixed_coord = TRUE)
pl