plotVolcano: Volcano plot for differential expression analysis

In genekitr: Gene Analysis Toolkit

Volcano plot for differential expression analysis

Description

Volcano plot for differential expression analysis

Usage

plotVolcano(
  deg_df,
  stat_metric = c("p.adjust", "pvalue"),
  stat_cutoff = 0.05,
  logFC_cutoff = 1,
  up_color = "#E31A1C",
  down_color = "#1F78B4",
  show_gene = NULL,
  dot_size = 1.75,
  ...
)

Arguments

deg_df	DEG dataframe with gene id, logFC and stat(e.g. pvalue/qvalue).
stat_metric	Statistic metric from "pvalue" or "p.adjust".
stat_cutoff	Statistic cutoff, default is 0.05.
logFC_cutoff	Log2 fold change cutoff, default is 1 which is actually 2 fold change.
up_color	Color of up-regulated genes, default is "dark red".
down_color	Color of down-regulated genes, default is "dark blue".
show_gene	Select genes to show, default is no genes to show.
dot_size	Volcano dot size, default is 1.75.
...	other arguments from 'plot_theme' function

Value

A ggplot object

Examples

if(requireNamespace("ggrepel",quietly = T)){
library(ggplot2)
data(deg, package = "genekitr")
plotVolcano(deg, "p.adjust", remove_legend = TRUE, dot_size = 3)

# show some genes
plotVolcano(deg, "p.adjust",
  remove_legend = TRUE,
  show_gene = c("CD36", "DUSP6", "IER3","CDH7")
)
}

genekitr documentation built on Sept. 11, 2024, 9:10 p.m.