multigroupVolcano: plot volcano given multiple conditions

In quantable: Streamline Descriptive Analysis of Quantitative Data Matrices

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

data(multigroupFCDATA)
colnames(multigroupFCDATA)
multigroupVolcano(multigroupFCDATA,effect="logFC",
type="adj.P.Val",condition="Condition",colour="colour",label="Name" )

Example output

loading package quantable
[1] "logFC"     "adj.P.Val" "Condition" "colour"    "Name"     

quantable documentation built on May 2, 2019, 4:05 p.m.