Plot sequence logo of a collection of sequences

Source: R/plot_arch_for_clusters.R

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
)

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_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)

#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.
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)

#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Scale for 'x' is already present. Adding another scale for 'x', which will
#> replace the existing scale.
#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.
#> Plot title: 
pl