Plot differentially expressed genes (DEGs) volcano — plot_deg

Plot differentially expressed genes (DEGs) volcano.

Usage

plot_deg_volcano(
  deg_file,
  id_col = "GeneID",
  fc_col = "log2FoldChange",
  sig_col = "padj",
  fc_threshold = 1,
  sig_threshold = 0.05,
  point_size = 2,
  point_alpha = 0.5,
  up_color = "#ff0000",
  down_color = "#008800",
  ns_color = "#888888"
)

Arguments

deg_file: DEG table from DESeq2 analysis.
id_col: Gene IDs column name. ("GeneID").
fc_col: Log2(fold change) column name. ("log2FoldChange").
sig_col: Significance column name. ("padj", "pvalue").
fc_threshold: Absolute log2FC threshold. (1).
sig_threshold: Significance threshold. (0.05).
point_size: Point size. (2).
point_alpha: Point alpha. (0.5).
up_color: Color for up-regulated significant genes. ("#ff0000").
down_color: Color for down-regulated significant genes. ("#008800").
ns_color: Color for non-significant genes. ("#888888").

Value

A ggplot object visualizing DEGs volcano.

Author

benben-miao

Examples

# DEG results from DESeq2
deg_file <- system.file(
  "extdata",
  "example.deg",
  package = "GAnnoViz")

# Volcano plot
plot_deg_volcano(
  deg_file = deg_file,
  id_col = "GeneID",
  fc_col = "log2FoldChange",
  sig_col = "padj",
  fc_threshold = 1,
  sig_threshold = 0.05,
  point_size = 2,
  point_alpha = 0.5,
  up_color = "#ff0000",
  down_color = "#008800",
  ns_color = "#888888"
)