Plot abundance versus interaction stoichiometries

Source: R/Plotting_functions.R

Plot abundance versus interaction stoichiometries

plot_2D_stoichio(res, condition = "max", 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 = "black",
  induced = "red", repressed = "blue", bait = "black"), shape = 21,
  stroke = 1, p_val_thresh = 0.05, fold_change_thresh = 1,
  ref_condition = res$conditions[1])

Arguments

res

an InteRactome
condition

condition selected. If "max", the maximum stoichiometry across conditions will be used.
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

Value

a plot