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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"),
  ht.color = "black",
  ht.shape = 17,
  ht.size = 1.5,
  ht.textcolor = "black",
  ht.textsize = 2,
  ...
)

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.

ht.color

A character string (default = "black") specifying the point color of highlighted proteins.

ht.shape

A numeric value (default = 17) specifying the point shape of highlighted points. See [ggplot2: Elegant Graphics for Data Analysis](https://ggplot2-book.org/scales-other.html#sec-scale-shape) for more details.

ht.size

A numeric value (default = 1.5) specifying the point size of highlighted proteins.

ht.textcolor

A character string (default = "black") specifying the font color of text labels for highlighted proteins.

ht.textsize

A numeric value (default = 2) specifying the font size of text labels for highlighted proteins.

...

Optional arguments passed to geom_text_repel.

Value

An object of class ggplot.