Plot a volcano plot of differential expression results.

Creates a volcano plot from the tibble returned by tidy_deseq_results(). Significant points are labeled with ggrepel::geom_text_repel().

Usage

plot_volcano(
  data,
  lab_col = "ref",
  padj_cutoff = 0.05,
  max_overlaps = 20,
  point_size = 1.5,
  label_size = 3,
  sig_color = "#D55E00",
  nonsig_color = "grey60"
)

Arguments

data

A tibble from tidy_deseq_results() with at least log2FoldChange, padj, and significant columns.

lab_col

Column name (string) used for point labels. Default "ref".

padj_cutoff

Numeric; draws a dashed horizontal line at -log10(padj_cutoff). Default 0.05.

max_overlaps

Maximum number of overlapping labels passed to ggrepel::geom_text_repel(). Default 20.

point_size

Numeric size for ggplot2::geom_point(). Default 1.5.

label_size

Numeric size for ggrepel::geom_text_repel(). Default 3.

sig_color

Color for significant points. Default "#D55E00".

nonsig_color

Color for non-significant points. Default "grey60".

Value

A ggplot object.

Examples

res <- tibble::tibble(
  ref = paste0("tRNA-", 1:10),
  log2FoldChange = rnorm(10),
  pvalue = c(rep(0.001, 3), rep(0.5, 7)),
  padj = c(rep(0.01, 3), rep(0.8, 7)),
  significant = c(rep(TRUE, 3), rep(FALSE, 7))
)
plot_volcano(res)