barcode_plot: Barcode plot

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Barcode plot

Description

Plots a "barcode plot" - a vertical line for each identified peptide. Peptides can be colored based on an additional variable. Also differential abundance can be displayed.

Usage

barcode_plot(
  data,
  start_position,
  end_position,
  protein_length,
  coverage = NULL,
  colouring = NULL,
  protein_id = NULL,
  facet = NULL,
  cutoffs = NULL
)

Arguments

data	Data frame containing differential abundance, start and end peptide or precursor positions and protein length.
start_position	Column in the data frame containing the start positions for each peptide or precursor.
end_position	Column in the data frame containing the end positions for each peptide or precursor.
protein_length	Column in the data frame containing the length of the protein.
coverage	Optional, column in the data frame containing coverage in percent. Will appear in the title of the barcode if provided.
colouring	Optional argument, column in the data frame containing information by which peptide or precursors should be colored.
protein_id	Optional argument, column in the data frame containing protein identifiers. Required if only one protein should be plotted and the data frame contains only information for this protein.
facet	Optional argument, column in the data frame containing information by which data should be faceted. This can be protein identifiers. Only 20 proteins are plotted at a time, the rest is ignored. If more should be plotted, a mapper over a subsetted data frame should be created.
cutoffs	Optional argument specifying the log2 fold change and significance cutoffs used for highlighting peptides. If this argument is provided colouring information will be overwritten with peptides that fulfill this condition. The cutoff should be provided in a vector of the form c(diff = 2, pval = 0.05). The name of the cutoff should reflect the column name that contains this information (log2 fold changes, p-values or adjusted p-values).

Value

A barcode plot is returned.

Examples

data <- data.frame(
  start = c(5, 40, 55, 130, 181, 195),
  end = c(11, 51, 60, 145, 187, 200),
  length = rep(200, 6),
  pg_protein_accessions = rep("Protein 1", 6),
  diff = c(1, 2, 5, 2, 1, 1),
  pval = c(0.1, 0.01, 0.01, 0.2, 0.2, 0.01)
)

barcode_plot(
  data,
  start_position = start,
  end_position = end,
  protein_length = length,
  facet = pg_protein_accessions,
  cutoffs = c(diff = 2, pval = 0.05)
)

protti documentation built on Jan. 22, 2023, 1:11 a.m.