protti: plot_peptide_profiles – R documentation

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plot_peptide_profiles

Peptide abundance profile plot

Description

Creates a plot of peptide abundances across samples. This is helpful to investigate effects of peptide and protein abundance changes in different samples and conditions.

Usage

plot_peptide_profiles(
  data,
  sample,
  peptide,
  intensity_log2,
  grouping,
  targets,
  protein_abundance_plot = FALSE,
  interactive = FALSE,
  export = FALSE,
  export_name = "peptide_profile_plots"
)

Arguments

`data`	Data frame containing at least the input variables.
`sample`	Column in the data frame containing sample names.
`peptide`	Column in the data frame containing peptide or precursor names.
`intensity_log2`	Column in the data frame containing log2 transformed intensities.
`grouping`	Column in the data frame containing groups by which the data should be split. This can be for example protein IDs.
`targets`	Character vector specifying elements of the grouping column which should be plotted. This can also be `"all"` if plots for all groups should be created. Depending on the number of elements in your grouping column this can be many plots.
`protein_abundance_plot`	Logical, if the input for this plot comes directly from `calculate_protein_abundance` this argument can be set to `TRUE`. This displays all peptides in gray, while the protein abundance is displayed in green.
`interactive`	A logical indicating whether the plot should be interactive (default is FALSE). If this is TRUE only one target can be supplied to the function. Interactive plots cannot be exported either.
`export`	A logical indicating if plots should be exported as PDF. The output directory will be the current working directory. The name of the file can be chosen using the `export_name` argument.
`export_name`	A character vector providing the name of the exported file if `export = TRUE`.

Value

A list of peptide profile plots.

Examples

## Not run: 
plot_peptide_abundance(
  data,
  sample = r_file_name,
  peptide = eg_precursor_id,
  intensity_log2 = log2_intensity,
  grouping = pg_protein_accessions,
  targets = c("P03421")
)

## End(Not run)

protti

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

v0.1.1

MIT + file LICENSE

Authors

Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

Initial release