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Rank abundance distribution plot (Whittaker plot)

Source: R/visualization.R
visualize.rank.Rd

Generate a rank abundance distribution plot, also known as Whittaker plot, for the data.

Usage

visualize.rank(
  dataSet,
  listName = c(),
  regexName = c(),
  by = NULL,
  facet = c("Condition", "Replicate"),
  color = "red",
  ...
)

Arguments

dataSet

A data frame containing the data signals.

listName

A character vector specifying proteins for exact matching to highlight.

regexName

A character vector specifying proteins for regular expression pattern matching to highlight.

by

A character string (default = "PG.ProteinName" for Spectronaut, default = "AccessionNumber" for Scaffold) specifying the information to which listName and/or regexName filter is applied. Allowable options include:

  • For Spectronaut: "PG.Genes", "PG.ProteinAccession", "PG.ProteinDescriptions", and "PG.ProteinName".

  • For Scaffold: "ProteinDescriptions", "AccessionNumber", and "AlternateID".

facet

A character string (default = c("Replicate", "Condition")) specifying grouping variables for faceting. Allowed values are:

  • "Condition": Abundance values are averaged across replicates.

  • "Replicate": Abundance values are averaged across conditions.

  • c("Condition", "Replicate"): No averaging is performed.

  • c("Replicate", "Condition"): No averaging is performed.

color

A character string (default = red") specifying the color used to highlight proteins.

...

Optional arguments passed to geom_text_repel.

Value

An object of class ggplot.