tandem MS data

plot_stoichio

R Documentation

Plot interaction stoichiometries per biological replicate

Description

Plot interaction stoichiometries per biological replicate

Usage

plot_stoichio(
  res,
  name,
  yvar = "stoichio_bio",
  conditions = res$conditions,
  ref_condition = conditions[1],
  test = "t.test",
  test.args = list(paired = FALSE),
  map_signif_level = c(`***` = 0.001, `**` = 0.01, `*` = 0.05),
  save_file = NULL,
  show_violin = TRUE,
  show_line = TRUE,
  theme_name = "theme_bw",
  n_labels_skip = 0,
  minor_ticks = 2:9
)

Arguments

`res`	an `InteRactome`
`name`	name of the protein to display
`yvar`	name of the y-axis variable. Either "stoichio_bio" or "norm_intensity_bio".
`conditions`	set of conditions to display
`ref_condition`	name of the reference condition for all `test`
`test`	name of the test function to compare sttoichiometries between conditions
`test.args`	arguments passed to function `test`
`map_signif_level`	named vector with labels and corresponding significance levels
`save_file`	path of output file (.pdf)
`show_violin`	logical. Display violin boxes?
`show_line`	logical. Dispaly lines?
`theme_name`	name of the ggplot2 theme function to use ('theme_gray' by default)
`n_labels_skip`	Number of labels skipped between two displayed labels on y axis.
`minor_ticks`	set of multiplicative factors used to generate minor ticks (set to 2:9 by default). Ignored if NULL.