Plots the coverage of proteins.

Usage

plot_protein_coverage(
  pr_matrix,
  genes,
  positions = NULL,
  zoom = NULL,
  fasta = NULL,
  organism = "hs",
  combine_overlap = T,
  dodge_labels = T,
  scaling = "centered"
)

Arguments

pr_matrix: The report.pr_matrix file.
genes: The gene names of the proteins that you would like to plot.
positions: A numeric vector indiciting the amino acid positions that you want to highlight.
zoom: A numeric with two values (start and stop) indicating the specific part of the protein that you want to plot.
fasta: Data frame with protein information when not using a default option. See get_ibaq_peptides
organism: Specifies which default protein database to use. 'hs' for human, or 'mm' for mouse.
combine_overlap: Boolean specifying whether to combine miscleaved peptides.
dodge_labels: Boolean specifying wheter position labels should be plotted on different heights so that they do not overlap in the plot.
scaling: Boolean value indicating whether the peptide intensities should be centered over the different replicates.

Value

A ggplot2 object showing the found peptides for a protein.

Examples

smad4 <- plot_protein_coverage(report.pr_matrix, 'SMAD4', positions = c(100, 150))
#> Warning: Duplicated aesthetics after name standardisation: ymin
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.

# Zoom in on first 200 AA of protein
smad4 <- plot_protein_coverage(report.pr_matrix, 'SMAD4', positions = c(100, 150), zoom = c(1, 200))
#> Warning: Duplicated aesthetics after name standardisation: ymin
#> Coordinate system already present. Adding new coordinate system, which will
#> replace the existing one.