Plot protein intensities per biological replicate and background

Plot protein intensities per biological replicate and background

plot_comparison(res, names, conditions = res$conditions, textsize = 4,
  ylims = NULL, mapping = "point", var_x = "bckg",
  var_facet_x = "cond", var_facet_y = "name", var_color = "bio",
  var_alpha = "missing", levels_x = c(res$bckg_ctrl, res$bckg_bait),
  labels_x = c(res$bckg_ctrl, res$bckg_bait), color_values = NULL,
  alpha_values = c(`TRUE` = 0.5, `FALSE` = 1), show_bar = FALSE,
  show_error_bar = FALSE, show_signif = TRUE, show_violin = TRUE,
  offset_bar = FALSE, comparisons = list(c(1, 2)), test = "t.test",
  test.args = list(paired = FALSE), map_signif_level = c(`***` = 0.001,
  `**` = 0.01, `*` = 0.05), position = "position_jitter",
  position.args = list(width = 0.3, height = 0))

Arguments

res	an InteRactome
names	name of the protein to display
conditions	set of conditions to display
textsize	size of labels corresponding to significance levels
ylims	plot limits on the y axis
mapping	name of the plot elemnet on which the aestethics color and alpha are mapped. Can be either "point" or "bar".
var_x	x variable
var_facet_x	variable used for faceting plots horizontally
var_facet_y	variable used for faceting plots vertically
var_color	variable used for the color aestethic
var_alpha	variable used for the alpha aestethic
levels_x	defines factor levels for x variable
labels_x	defines the labels for the levels of the x variable
color_values	named vector of colors.
alpha_values	named vector of alpha values.
show_bar	logical, show bars using geom_bar
show_error_bar	logical, show error bars using geom_errorbar
show_signif	logical, show significance of comparison tests using geom_signif
show_violin	logical, show point distribution using geom_violin
offset_bar	logical, use an offset to ensure all values are positive
comparisons	list of comparison pairs (as indices or x variable names)
test	name of the test function to compare intensities between background
test.args	arguments passed to function test()
map_signif_level	named vector with labels and corresponding significance levels
position	name of the function used to position data points
position.args	arguments passed to function position()

Value

a plot