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Volcano Plot

Source: R/viz_volcano.R
bb_volcano.Rd

Creates a publication-ready volcano plot from differential expression results.

Usage

bb_volcano(
  de_result,
  fc_cutoff = 1,
  p_cutoff = 0.05,
  label_genes = NULL,
  n_label = 10L,
  point_size = 1,
  colors = c(up = "#D73027", down = "#4575B4", ns = "grey70")
)

Arguments

de_result

A data.frame with columns gene, log2fc, pvalue, padj. Typically the output of bb_deseq2(), bb_edger(), or bb_limma_voom().

fc_cutoff

Numeric. Absolute log2 fold-change cutoff for significance. Default 1.

p_cutoff

Numeric. Adjusted p-value cutoff for significance. Default 0.05.

label_genes

Character vector. Specific gene names to label on the plot. If NULL (default), the top n_label significant genes are labeled.

n_label

Integer. Number of top significant genes to auto-label when label_genes is NULL. Default 10.

point_size

Numeric. Size of points. Default 1.

colors

Named character vector of length 3 for up, down, and non-significant colors.

Value

A ggplot2::ggplot object.

Examples

de <- data.frame(
  gene = paste0("gene", 1:200),
  log2fc = rnorm(200, 0, 2),
  pvalue = 10^(-runif(200, 0, 5)),
  padj = 10^(-runif(200, 0, 4))
)
bb_volcano(de)
#> Warning: Removed 190 rows containing missing values or values outside the scale range
#> (`geom_text_repel()`).