draw_volcano: draw a volcano plot

In tinyarray: Expression Data Analysis and Visualization

draw a volcano plot

Description

print a volcano plot for Differential analysis result in data.frame format.

Usage

draw_volcano(
  deg,
  lab = NA,
  xlab.package = TRUE,
  pvalue_cutoff = 0.05,
  logFC_cutoff = 1,
  pkg = 1,
  adjust = FALSE,
  symmetry = FALSE,
  color = c("#2874C5", "grey", "#f87669")
)

Arguments

deg	a data.frame created by Differential analysis
lab	label for x axis in volcano plot, if NA , x axis names by package
xlab.package	whether to use the package name as the x axis name
pvalue_cutoff	Cutoff value of pvalue,0.05 by default.
logFC_cutoff	Cutoff value of logFC,1 by default.
pkg	a integer ,means which Differential analysis packages you used,we support three packages by now, 1,2,3,4 respectively means "DESeq2","edgeR","limma(voom)","limma"
adjust	a logical value, would you like to use adjusted pvalue to draw this plot,FAlSE by default.
symmetry	a logical value ,would you like to get your plot symmetrical
color	color vector

Value

a volcano plot according to logFC and P.value(or adjust P.value)

Author(s)

Xiaojie Sun

See Also

draw_heatmap;draw_pca;draw_venn

Examples

head(deseq_data)
draw_volcano(deseq_data)
draw_volcano(deseq_data,pvalue_cutoff = 0.01,logFC_cutoff = 2)
draw_volcano(deseq_data,color = c("darkgreen", "darkgrey", "#B2182B"))

tinyarray documentation built on Aug. 18, 2023, 9:07 a.m.