tandem MS data

plot_volcanos

R Documentation

Plot protein enrichement fold-change versus p-value

Description

Plot protein enrichement fold-change versus p-value

Usage

plot_volcanos(
  res = NULL,
  data = NULL,
  names = NULL,
  idx = NULL,
  labels = NULL,
  show_all_above_thresh = FALSE,
  N_print = 15,
  conditions = NULL,
  p_val_thresh = 0.05,
  fold_change_thresh = 2,
  x0 = NULL,
  c = NULL,
  save_file = NULL,
  xlim = NULL,
  ylim = NULL,
  norm = FALSE,
  both_sides = FALSE,
  show_thresholds = TRUE,
  alpha_segment = 0.2,
  theme_name = "theme_bw",
  size = 1,
  alpha = 1,
  color = rgb(0.75, 0.75, 0.75),
  label_size = 3,
  n_character_max = 8,
  n_labels_skip_x = 0,
  n_labels_skip_y = 1,
  minor_ticks = 2:9,
  ...
)

Arguments

`res`	an `InteRactome`
`data`	data.frame with columns 'names', 'p_val' and 'fold_change'
`names`	Names of proteins highlighted
`idx`	indices of proteins highlighted (superseeds `names`)
`labels`	labels for proteins in plot. Must the same length as `res$names` or `data$names`
`show_all_above_thresh`	logical. Highlight all proteins above threshold?
`N_print`	maximum of protein labels to display
`conditions`	conditions to plot
`p_val_thresh`	threshold on p-value to display
`fold_change_thresh`	threshold on fold-change to display
`x0`	parameters x0 of the line dividing the volcano plot according to `f(x) = c / (\|x\|-x0)`. Ignored unless parameters `p_val_thresh` and `fold_change_thresh` are set to `NULL`
`c`	parameters c of the line dividing the volcano plot according to `f(x) = c / (\|x\|-x0)`. Ignored unless parameters `p_val_thresh` and `fold_change_thresh` are set to `NULL`
`save_file`	path of output file (.pdf)
`xlim`	range of x values
`ylim`	range of y values
`norm`	Use normalized fold-changes
`both_sides`	logical. Shading on right and left upper graphs.
`show_thresholds`	Show thresholds using red lines?
`alpha_segment`	transparency of threshold segments
`theme_name`	name of the ggplot2 theme function to use ('theme_gray' by default)
`size`	dot size
`alpha`	dot transparency
`color`	dot color
`label_size`	size of labels (5 by default)
`n_character_max`	max number of label characters
`n_labels_skip_x`	Number of labels skipped between two displayed labels on x axis.
`n_labels_skip_y`	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.
`...`	parameters passed to `geom_text_repel()`