plot_coverage: Plot peptide coverage

In HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Description

Plots the peptide coverage of the protein sequence.

Usage

plot_coverage(
  dat,
  protein = dat[["Protein"]][1],
  chosen_state = dat[["State"]][1]
)

Arguments

dat	data as imported by the read_hdx function
protein	protein to be included in plot
chosen_state	sequence states to be included in plot

Details

The function plot_coverage plots sequence coverage based on experimental data for chosen protein in chosen state. Only non-duplicated peptides are shown on the plot, next to each other.

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

Value

a ggplot object.

See Also

read_hdx plot_position_frequency

Examples

# load example data
dat <- read_hdx(system.file(package = "HaDeX", 
                            "HaDeX/data/KD_180110_CD160_HVEM.csv"))
                            
# plot coverage with default parameters
plot_coverage(dat)

# plot coverage with explicit parameters
plot_coverage(dat, protein = "db_CD160", chosen_state = "CD160_HVEM")

HaDeX documentation built on Aug. 12, 2021, 5:20 p.m.