Visualize a given (PWM) matrix as a sequence logo.

Visualize a given (PWM) matrix as a sequence logo.

plot_ggseqlogo(
  pwm_mat,
  method = "bits",
  pos_lab = NULL,
  pdf_name = NULL,
  bits_yax = "full",
  fixed_coord = FALSE
)

Arguments

pwm_mat	Matrix (usually a PWM, but can be any non-normalized matrix) to be represented as a sequence logo.
method	For ggseqlogo; either of 'custom', 'bits', or 'probability'. Default is 'bits'.
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.
pdf_name	Name of the file which will be saved as PDF.
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	Set this to TRUE to use a fixed aspect ratio for the plot. Default is FALSE.

Value

A ggplot2 object so you can simply call print or save on it later. If pdf_name is given, it is also saved in addition to returning the ggplot object.

See also

plot_ggheatmap for plotting PWMs as heatmaps, plot_ggseqlogo_of_seqs for visualizing a collection of sequences by their sequence logo.

Other visualization functions: plot_ggheatmap(), viz_bas_vec_heatmap_seqlogo(), viz_seqs_acgt_mat_from_seqs()

Examples

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

pwm <- archR::make_dinuc_PWMs(get_clBasVec_m(res,iter=1)[,1], 
                        add_pseudo_counts = FALSE)

plot_ggseqlogo(pwm_mat = pwm, 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.