Step: Logo Plot

Create a logo plot for glycosylation sites using glyvis::plot_logo(). The logo plot visualizes the amino acid sequence patterns around glycosylation sites. This step is only applicable for glycoproteomics experiments.

Usage

step_logo(
  on = "exp",
  n_aa = 5L,
  fasta = NULL,
  plot_width = 5,
  plot_height = 3,
  ...
)

Arguments

on: Name of the experiment data in ctx$data to plot. One of "exp", "sig_exp". Default is "exp".
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.
plot_width: Width of the plot in inches. Default is 5.
plot_height: Height of the plot in inches. Default is 3.
...: Additional arguments passed to ggseqlogo::ggseqlogo().

Value

A glysmith_step object.

Details

Data required:

Depends on on parameter (default: exp)

Plots generated:

logo: A logo plot (if on = "exp")
sig_logo: A logo plot (if on = "sig_exp")

AI Prompt

This section is for AI in inquire_blueprint() only.

Include this step if the user explicitly asks for logo plot.
If used, ask user if a FASTA file is provided. Tell the user that if not, protein sequences will be fetched from Uniprot automatically.

Examples