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Logo Plot

plot_logo.Rd

Draw a logo plot for all glycosites. Positions with insufficient flanking amino acids will be padded with "X". Currently supported data types:

  • glyexp_experiment: Experiment created by glyexp::experiment(). Logo plot of glycosylation sites is plotted.

Usage

plot_logo(x, n_aa = 5L, fasta = NULL, tax_id = 9606L, ...)

# S3 method for class 'glyexp_experiment'
plot_logo(x, n_aa = 5L, fasta = NULL, tax_id = 9606L, ...)

Arguments

x

An object to be plotted.

n_aa

The number of amino acids to the left and right of the glycosylation site. For example, if n_aa = 5, the resulting sequence will contain 11 amino acids.

fasta

The path to the FASTA file containing protein sequences. If glyclean::add_site_seq() has been called on the experiment, this argument can be omitted. When site_sequence is missing and fasta is NULL, UniProt.ws is used to fetch protein sequences automatically.

tax_id

The NCBI taxonomy ID used for UniProt.ws lookups. Defaults to 9606.

...

Additional arguments passed to ggseqlogo::ggseqlogo().

Value

A ggplot object.

See also

ggseqlogo::ggseqlogo()