Plots the coverage of proteins.

Usage

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

Arguments

se: The SummarizedExperiment object from prepare_se.
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.
condition_order: Character vector that specifies the order of the conditions on the y-axis.

Value

A ggplot2 object showing the found peptides for a protein.

Examples

se <- prepare_se(report.pg_matrix, expDesign, report.pr_matrix)

#> Imputing along margin 2 (samples/columns).
#> [1] 0.3066195
#> Imputing along margin 1 (features/rows).
#> Warning: 36 rows with more than 50 % entries missing;
#>  mean imputation used for these rows
#> Cluster size 5574 broken into 3662 1912 
#> Cluster size 3662 broken into 1462 2200 
#> Done cluster 1462 
#> Cluster size 2200 broken into 1110 1090 
#> Done cluster 1110 
#> Done cluster 1090 
#> Done cluster 2200 
#> Done cluster 3662 
#> Cluster size 1912 broken into 1379 533 
#> Done cluster 1379 
#> Done cluster 533 
#> Done cluster 1912 
smad4 <- plot_protein_coverage(se, 'SMAD4', positions = c(100, 150))
#> Warning: Duplicated aesthetics after name standardisation: ymin
#> Coordinate system already present.
#> ℹ Adding new coordinate system, which will replace the existing one.

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