Create Volcano Plot

Create a volcano plot given a vector of log2-transformed fold-changes (FC) and linear space p-values.

Usage

plotVolcano(
  data,
  FC,
  p.value,
  labels,
  identify = FALSE,
  fc.cutoff = 1,
  pt.size = 2.5,
  text.size = 3,
  cutoff = 0.05/nrow(data),
  main = NULL,
  x.lab = NULL,
  ...
)

Arguments

data

A data.frame object containing at least two columns containing 1) log2-transformed fold-changes, 2) linear-space p-values. A third column containing point labels must be supplied, if identify = TRUE.

FC

An unquoted string identifying the column in data containing a vector log2()-transformed fold-changes.

p.value

An unquoted string identifying the column in data containing a vector of p-values.

labels

An unquoted string identifying the column in data containing point labels, typically "Target" or "Analyte" names.

identify

Logical. Should significant points be identified?

fc.cutoff

Placement for the cutoff for coloring points along the fold-change x-axis. Defaults to doubling in fold-change (1).

pt.size

Numeric. The size for the points.

text.size

Numeric. The size for the identifying text.

cutoff

Horizontal statistical significance cutoff for coloring points. Defaults to Bonferroni corrected significance at alpha = 0.05 in "p-value" linear space [0, 1].

main

Character. Main title for the plot. See ggtitle() for ggplot2 style graphics.

x.lab

Character. Optional string for the x-axis. Otherwise one is automatically generated (default).

...

Arguments passed to geom_point().

See also

geom_point().

Other volcano: plotVolcanoHTML()

Author

Stu Field

Examples

withr::with_seed(101, {
  fc1 <- sort(runif(500, -2.5, 0))   # Z-scores as dummy fold-changes
  fc2 <- sort(runif(500, 0, 2.5))    # Z-scores as dummy fold-changes
  p1  <- pnorm(fc1)                  # p-values for neg. scores
  p2  <- pnorm(fc2, lower.tail = FALSE) # p-values for pos. scores
  p   <- jitter(c(p1, p2), amount = 0.1) # add noise
  p[p < 0] <- runif(sum(p < 0), 1e-05, 1e-02) # floor p > 0 after jitter
  df <- data.frame(fc = c(fc1, fc2), p = p)
})

plotVolcano(df, fc, p, cutoff = 0.1)  # lower p-value cutoff


# add some random labels to `df`
df <- dplyr::mutate(df, pt_label = dplyr::row_number())
plotVolcano(df, fc, p, labels = pt_label, identify = TRUE, cutoff = 0.01)