tandem MS data

plot_2D_stoichio

R Documentation

Plot abundance versus interaction stoichiometries

Description

Plot abundance versus interaction stoichiometries

Usage

plot_2D_stoichio(
  res,
  labels = NULL,
  condition = "max",
  names = NULL,
  idx_rows = 1:30,
  xlim = NULL,
  ylim = NULL,
  N_display = 30,
  only_interactors = FALSE,
  fill_values = c(not_regulated = "black", induced = "red", repressed = "blue", bait =
    "yellow"),
  color_values = c(not_regulated = "", induced = "", repressed = "", bait = "black"),
  shape = 21,
  stroke = 1,
  p_val_thresh = 0.05,
  fold_change_thresh = 1,
  ref_condition = res$conditions[1],
  label_size_min = 1,
  label_size_max = 3,
  label_size_scale_factor = 25,
  label_range = NULL,
  theme_name = "theme_bw",
  show_core = TRUE,
  range_factor = 1.1,
  ratio_strong = 0.3,
  n_character_max = 8,
  n_labels_skip = 0,
  minor_ticks = 2:9,
  ...
)

Arguments

`res`	an `InteRactome`
`labels`	labels for proteins in plot. Must the same length as `res$names`
`condition`	condition selected. If "max", the maximum stoichiometry across conditions will be used.
`names`	names of the proteins to display. If not NULL, supersedes `N_display` and `only_interactors`
`idx_rows`	numeric vector to select proteins to display
`xlim`	range of x values
`ylim`	range of y values
`N_display`	maximum number of protein to display
`only_interactors`	display only interactors (identified using the function `identify_interactors()`)
`fill_values`	color vector passed to `scale_fill_manual()`
`color_values`	color vector passed to `scale_color_manual()`
`shape`	Point shape aesthetics passed to `geom_point()`
`stroke`	Point stroke aesthetics passed to `geom_point()`
`p_val_thresh`	Threshold on p-value used to identify regulated interactions
`fold_change_thresh`	Threshold on fold-change used to identify regulated interactions
`ref_condition`	Reference condition used to identify regulated interactions
`label_size_min`	minimum label size (between 0 and `label_size_max`)
`label_size_max`	maximum label size (a threshold on log10(fold-change))
`label_size_scale_factor`	scale label size according to plot range (the higher the bigger the label)
`label_range`	if NULL, scales labels according to plot range (in log10 scale).
`theme_name`	name of the ggplot2 theme function to use ('theme_gray' by default)
`show_core`	logical. Show core interaction area?
`range_factor`	numeric factor to expand plot range
`ratio_strong`	ratio of available proteins bound to bait usd to define gray-shaded area
`n_character_max`	max number of label characters (ignored if NULL)
`n_labels_skip`	Number of labels skipped between two displayed labels on x and y axis.
`minor_ticks`	set of multiplicative factors used to generate minor ticks (set to 2:9 by default). Ignored if NULL.
`...`	parameters passed to `geom_text_repel()`