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Volcano Plot of Differential Expression Results

PlotVolcano.Rd

Produces a publication-ready volcano plot from a DEG data frame (presto, FindMarkers, or any table with logFC and adjusted p-value columns). Automatically detects column names for common output formats. Points are colored by direction × significance; top genes per direction are labeled with ggrepel.

Usage

PlotVolcano(
  deg_df,
  gene.column = NULL,
  fc.column = NULL,
  padj.column = NULL,
  group.by = NULL,
  ncol = NULL,
  fc.cutoff = 0.25,
  padj.cutoff = 0.05,
  top.n.labels = 10,
  highlight.genes = NULL,
  colors = c(up = "#B40426", down = "#3B4CC0", ns = "gray70"),
  point.size = 1,
  point.alpha = 0.6,
  max.overlaps = 20,
  output_dir = NULL,
  object_name = "",
  subset_name = "",
  file_name = NULL,
  width = NULL,
  height = NULL,
  timestamp = FALSE
)

Arguments

deg_df

Data frame with differential expression results. Compatible with presto ("feature"/"logFC"/"padj") and Seurat ("gene"/"avg_log2FC"/"p_val_adj").

gene.column

Column with gene names. Auto-detected if NULL.

fc.column

Column with log fold-change. Auto-detected if NULL.

padj.column

Column with adjusted p-value. Auto-detected if NULL.

group.by

Optional column to facet by (one panel per group level). NULL = no faceting.

ncol

Integer or NULL. Number of columns in the facet layout when group.by is set. NULL lets ggplot2 choose.

fc.cutoff

Absolute log fold-change threshold (vertical dashed lines). Default 0.25.

padj.cutoff

Adjusted p-value significance cutoff (horizontal dashed line). Default 0.05.

top.n.labels

Number of top genes to label per direction (up and down separately). Genes ranked by \(-\log_{10}(padj) \times |logFC|\). Default 10.

highlight.genes

Character vector of specific genes to always label regardless of their ranking.

colors

Named character vector with elements "up", "down", and "ns" (not significant). Defaults to red/blue/gray.

point.size

Point size. Default 1.

point.alpha

Point transparency. Default 0.6.

max.overlaps

Maximum label overlaps passed to ggrepel. Default 20.

output_dir

Directory to save a PDF. NULL = plot only, no save.

object_name

Label prefix for the output file name.

subset_name

Optional subset label appended to the file name.

file_name

Character or NULL. Base name (no extension) for the saved PDF. NULL (default) auto-deduces from object_name, subset_name, and group.by.

width, height

Numeric or NULL. Override the auto-calculated PDF dimensions in inches. NULL (default) auto-sizes to the facet grid.

timestamp

Logical. When TRUE, append a _YYYYMMDD-HHMMSS stamp to the saved file name so repeated runs are versioned instead of overwriting the previous PDF. Default FALSE.

Value

A ggplot2 object (invisibly if saved). Printed to the active device.