plot volcano given multiple contrasts

plot volcano given multiple contrasts

Usage

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

.data

data in long format

effect

column containing effect sizes

significance

column containing p-values, q.values etc

contrast

column with contrast

colour

colouring of points

xintercept

fc thresholds

yintercept

significance threshold

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

maxNrOfSignificantText

maximum number of significant labels to display

See also

Other utilities: INTERNAL_FUNCTIONS_BY_FAMILY, get_UniprotID_from_fasta_header(), matrix_to_tibble(), names_to_matrix(), pairs_smooth(), pairs_w_abline(), panel_cor(), panel_hist(), remove_NA_rows(), table_facade()

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)