tandem MS data

plot_comparison

R Documentation

Plot protein intensities per biological replicate and background

Description

Plot protein intensities per biological replicate and background

Usage

plot_comparison(
  res,
  names,
  conditions = res$conditions,
  textsize = 4,
  auto_scale = TRUE,
  ylims = NULL,
  mapping = "point",
  var_x = "bckg",
  var_facet_x = "cond",
  var_facet_y = "name",
  facet_scales = "free",
  var_color = "bio",
  var_alpha = "missing",
  levels_x = c(res$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),
  theme_name = "theme_bw",
  n_labels_skip = 0,
  minor_ticks = 2:9
)

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
`auto_scale`	logical. Set y axis limits automatically for all plots?
`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
`facet_scales`	option passed to `facet_grid()` used for scaling data across facets
`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()`
`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.