quantable (version 0.3.6)

multigroupVolcano: plot volcano given multiple conditions

Description

plot volcano given multiple conditions

Usage

multigroupVolcano(misspX, effect = "fc", type = "p.adjust",
  condition = "condition", colour = "colour", xintercept = c(-2, 2),
  pvalue = 0.05, label = NULL, size = 1, segment.size = 0.3,
  segment.alpha = 0.3, ablines = data.frame(fc = c(0, 0), p = c(0.01, 0.05),
  Area = c("p=0.01", "p=0.05")))

Arguments

misspX

data in long format

effect

column containing effect sizes

type

column containing p-values, q.values etc

condition

column with condition

colour

colouring of points

xintercept

fc thresholds

pvalue

pvalue threshold

label

column containing labels

size

controls size of text

segment.size

controls size of lines

segment.alpha

controls visibility of lines

ablines

adds ablines horizontal and vertical

Examples

# NOT RUN {
data(multigroupFCDATA)
colnames(multigroupFCDATA)
multigroupVolcano(multigroupFCDATA,effect="logFC",
type="adj.P.Val",condition="Condition",colour="colour",label="Name" )
# }