Description Usage Arguments Value See Also Examples
View source: R/plot_ggheatmap.R
Visualize a given (PWM) matrix as a sequence logo.
1 2 3 4 5 6 7 8 | plot_ggseqlogo(
pwm_mat,
method = "bits",
pos_lab = NULL,
pdf_name = NULL,
bits_yax = "full",
fixed_coord = FALSE
)
|
pwm_mat |
Matrix (usually a PWM, but can be any non-normalized matrix) to be represented as a sequence logo. |
method |
For |
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. |
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.
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()
1 2 3 4 5 6 7 | 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)
|
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