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Rank abundance distribution plot (Whittaker plot)

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

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

Usage

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

Arguments

dataSet

The 2d data set of data.

listName

A character vector of proteins 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", "Replicate", c("Condition", "Replicate"), c("Replicate", "Condition"), or "none" for no grouping.

color

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

Value

An object of class ggplot.