plot volcano given multiple contrasts

multigroup_volcano(
  .data,
  effect = "fc",
  significance = "p.adjust",
  contrast = "condition",
  colour = "colour",
  xintercept = c(-2, 2),
  yintercept = 0.05,
  label = NULL,
  size = 1,
  segment.size = 0.3,
  segment.alpha = 0.3,
  scales = "fixed",
  maxNrOfSignificantText = 20
)

Arguments

effect

column containing effect sizes

contrast

column with contrast

colour

colouring of points

xintercept

fc thresholds

label

column containing labels

size

controls size of text

segment.size

controls size of lines

segment.alpha

controls visibility of lines

scales

parameter to ggplot2::facet_wrap

misspX

data in long format

p.value

column containing p-values, q.values etc

sigthreshold

sigthreshold threshold

ablines

adds ablines horizontal and vertical

Examples



show <- data.frame(logFC = rnorm(100, 0, 1), adj.P.Val = runif(100,0,1), Condition = sample(c("a","b")), colour = "forward", Name = paste0("n", 1:100))
prolfqua::multigroup_volcano( show,
effect="logFC",
significance = "adj.P.Val",
contrast="Condition",
colour=NULL,
label="Name",
maxNrOfSignificantText = 300)