Dot plot representation of interaction as a function of experimental conditions

Source: R/Plotting_functions.R

Dot plot representation of interaction as a function of experimental conditions

plot_per_condition(res, names = NULL,
  idx_cols = 1:length(res$conditions), idx_rows = 1:20,
  size_var = "norm_stoichio", size_range = c(0, 5.5),
  size_limits = c(0, 1), color_var = "p_val", color_breaks = c(1,
  0.1, 0.05, 0.01), color_values = c("black", "blue", "purple", "red"),
  color_default = 1, save_file = NULL, plot_width = 2.5 +
  length(res$conditions)/5, plot_height = 2 + length(idx_rows)/5,
  clustering = FALSE, ...)

Arguments

res

an InteRactome
names

vector of names to be displayed
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
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
...

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)

Value

a list conataining :

a plot "plot"

a numeric vector "idx_order" containing the position of the protein displayed within the InteRactome