volcano_plot: Volcano Plot

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Volcano Plot

Description

Volcano Plot

Usage

volcano_plot(
  x,
  y,
  xlab = "Log2 Fold Change",
  ylab = "-log10(Adjusted P)",
  lg2fc = 1,
  p = 0.05,
  restrict.vector = NA,
  label = NA,
  title = "",
  col.pal = c("blue", "gray", "red"),
  point.size = 2,
  alpha = 1
)

Arguments

x	Log2 Fold Change
y	Adjusted P value
xlab	Default "Log2"
ylab	Default "-log10(Adjusted P)"
lg2fc	Default cufoff 1
p	Default cutoff 0.05
restrict.vector	A TURE/FALSE factor. Only show TRUE point in the vector.
label	Point names which you want to show in plot. If you don't want to show, set NA
col.pal	Default: c("blue", "gray", "red"). A vector with 3 elements. For significantly down, not significant, significantly up
point.size	Default 2
alpha	Color alpha. Default 1

Examples

loonR::volcano_plot( tissue.exp.df.res$logFC, tissue.exp.df.res$adj.P.Val, lg2fc = 0.5, p = 0.05, label = label, restrict.vector = (tissue.exp.df.res$AUC > 0.7 & tissue.exp.df.res$AveExpr > 10)  )

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.