tandem MS data

plot_per_condition

R Documentation

Dot plot representation of interaction as a function of experimental conditions

Description

Dot plot representation of interaction as a function of experimental conditions

Usage

plot_per_condition(
  res,
  labels = NULL,
  names = NULL,
  idx_cols = 1:length(res$conditions),
  idx_rows = NULL,
  size_var = "norm_stoichio",
  size_range = c(0, 5.5),
  size_limits = c(0, 1),
  color_var = NULL,
  color_breaks = NULL,
  color_values = c("black", "blue", "purple", "red"),
  color_default = 1,
  color_max = NULL,
  save_file = NULL,
  plot_width = 2.5 + length(res$conditions)/5,
  plot_height = 2 + length(idx_rows)/5,
  clustering = FALSE,
  theme_name = "theme_bw",
  n_character_max = 8,
  ...
)

Arguments

`res`	an `InteRactome`
`labels`	labels for proteins in plot. Must the same length as `res$names`
`names`	Deprecated. Same as parameter `labels`.
`idx_cols`	numeric vector to select and order conditions to be displayed
`idx_rows`	numeric vector to select proteins to display
`size_var`	name of the variable corresponding to dot size
`size_range`	range of dot sizes to display
`size_limits`	limits used for the dot size scale
`color_var`	name of the variable corresponding to dot color
`color_breaks`	vector used to discretize colors
`color_values`	values parameter passed to `scale_color_manual()`
`color_default`	value corresponding to the default color
`color_max`	If not NULL, Hide dots with a color parameter above this threshold.
`save_file`	path of output file (.pdf)
`plot_width`	width of the output .pdf file
`plot_height`	height of the output .pdf file
`clustering`	logical or numeric vector. If logical, use hierarchical
`theme_name`	name of the ggplot2 theme function to use ('theme_gray' by default)
`n_character_max`	max number of label characters (ignored if NULL)
`...`	additionnal arguments passed to `dot_plot()` clustering to order proteins. If numeric, ordering indexes for displayed proteins (must be the same length as `idx_rows`)