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Peptide coverage

plot_coverage.Rd

Plot the peptide coverage of the protein sequence

Usage

plot_coverage(
  dat,
  protein = dat[["Protein"]][1],
  states = NULL,
  show_blanks = TRUE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

dat

data imported by the read_hdx function

protein

selected protein

states

selected biological states for given protein

show_blanks

logical, indicator if the non-covered regions of the sequence are indicated in red

interactive

logical, whether plot should have an interactive layer created with with ggiraph, which would add tooltips to the plot in an interactive display (HTML/Markdown documents or shiny app)

Value

a ggplot object

Details

The function plot_coverage generates sequence coverage plot based on experimental data for selected protein in selected biological states. Only non-duplicated peptides are shown on the plot, next to each other.

The aim of this plot is to see the dependence between position of the peptide on the protein sequence. Their position on y-axis does not contain any information.

See also

read_hdx plot_position_frequency

Examples

plot_coverage(alpha_dat)

plot_coverage(alpha_dat, show_blanks = FALSE)


diff_uptake_dat <- create_diff_uptake_dataset(alpha_dat)
plot_coverage(diff_uptake_dat)