Volcano: Volcano plot for every group comparison

In CHKim5/LMSstat: AUTOMATION OF STATISTICAL TESTS WITH AN IDENTICAL DATA INPUT.

Description

Volcano plot for every group comparison

Usage

Volcano(
  data,
  asterisk = "t-test",
  reverse = F,
  fig_width = NA,
  FC_log = 2,
  pval_log = 10,
  fig_height = NA,
  dotsize = 2,
  fixed_limit = F,
  x_limit = c(-15, 15),
  y_limit = c(-2, 6),
  pval_intercept = 0.05,
  max_overlap = 20,
  FC_range = c(-1.5, 1.5),
  sig_label = T,
  color = c("blue", "black", "red")
)

Arguments

data	data inheriting from Allstats
asterisk	statistics inheriting from Allstats # "t-test", "u-test", "Scheffe", "Dunn"
reverse	reverse the direction of fold change
fig_width	figure size
FC_log	Fold change log transformation value
pval_log	p_value log transformation value
fig_height	figure size
dotsize	dotsize
fixed_limit	whether the limit should be fixed or not T, F
x_limit	x axis limt c( -3,3)
y_limit	y axis limit c(0, 100)
pval_intercept	intercept for identification 0.05
max_overlap	maximum overlap for labels
FC_range	significant fold change range
sig_label	label significant variables
color	colors used for ggplots.color=c("#FF3300","#FF6600","#FFCC00","#99CC00","#0066CC","#660099")

Value

Volcano Plot

Examples

data(Data)
Test<-Allstats(Data)
Volcano(Test,asterisk = "t-test")

CHKim5/LMSstat documentation built on Dec. 17, 2021, 12:55 p.m.