multigroup_volcano: plot volcano given multiple contrasts

In wolski/prolfqua: Proteomics Label Free Quantification

plot volcano given multiple contrasts

Description

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

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

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)

wolski/prolfqua documentation built on Oct. 31, 2024, 9:22 a.m.