plot_ggseqlogo_of_seqs: Plot sequence logo of a collection of sequences

In snikumbh/seqArchR: Identify Different Architectures of Sequence Elements

Plot sequence logo of a collection of sequences

Description

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

Usage

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

Arguments

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.

Value

A sequence logo plot of the given DNA sequences.

See Also

plot_arch_for_clusters for obtaining multiple sequence logo plots as a list.

Examples

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

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