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Single volcano plot for PhosphoTRAP / TRAP-seq differential expression results

Source: R/ptrap_volcano.R
ptrap_volcano.Rd

A volcano plot puts log2 fold change (logFC, x-axis) against statistical significance (-log p-value, y-axis). Genes that are both strongly enriched and statistically reliable appear in the upper corners — the most biologically meaningful candidates. Genes that fail either threshold are shown in grey; those that pass both are coloured by direction ("UP" for enriched in IP, "DOWN" for depleted).

Usage

ptrap_volcano(
  de_result,
  fdr = TRUE,
  lfc_threshold = 1,
  fdr_threshold = 0.05,
  log_base = 10,
  gene_col = "Gene",
  treatment_col = "treatment",
  region_col = "BrainRegion",
  colors = NULL,
  point_size = 3.5,
  point_alpha = 0.7,
  genes.annot = NULL,
  max_overlaps = 20,
  title = NULL,
  interactive = FALSE
)

Arguments

de_result

A tibble returned by ptrap_de(). For test_method = "paired.ttest", pass the $results component.

fdr

Logical. If TRUE (default), significance is assessed using FDR (false discovery rate — multiple-testing adjusted p-value); if FALSE, uses raw PValue.

lfc_threshold

Minimum absolute log2 fold change for a gene to be coloured as DE. A value of 1 means at least a 2× change. Default 1.

fdr_threshold

Significance cutoff applied to the column selected by fdr. Default 0.05.

log_base

Numeric. Base of the logarithm for the p-value axis. Base 10 (default) is conventional; base 2 matches Tan et al. (2016). Must be a positive number other than 1.

gene_col

Column name for gene identifiers. Default "Gene".

treatment_col

Column name for treatment label. Default "treatment".

region_col

Column name for brain region label. Default "BrainRegion".

colors

Named vector mapping "UP" and "DOWN" to colours. Default is colourblind-friendly: "#0072b2" (UP), "#E69f00" (DOWN).

point_size

Size of points. Default 3.5.

point_alpha

Opacity of highlighted points. Default 0.7.

genes.annot

Character vector of gene names to label. In static mode labels are drawn via ggrepel::geom_text_repel(); in interactive mode they are omitted (use the hover tooltip instead). Default NULL.

max_overlaps

Passed to ggrepel::geom_text_repel(). Default 20.

title

Plot title. Auto-generated from region and treatment if NULL.

interactive

Logical. If TRUE, returns an interactive plotly::ggplotly() object with hover tooltips showing gene name, logFC, p-value, and FDR. Gene labels (genes.annot) are omitted in this mode. Default FALSE.

Value

A ggplot2::ggplot() object, or a plotly object when interactive = TRUE.

Details

Takes a single tibble from ptrap_de() (for test_method = "paired.ttest", pass the $results component). Gene labels are drawn only for genes listed in genes.annot, via ggrepel::geom_text_repel() (static mode only). The DE classification is recomputed inside this function from the supplied thresholds, so you can explore different cutoffs without re-running ptrap_de().

Examples

if (FALSE) { # \dontrun{
# Default: -log10(FDR), static
ptrap_volcano(res)

# Raw p-values, log2 scale -- as in Tan et al. 2016
ptrap_volcano(res, fdr = FALSE, log_base = 2)

# Interactive with hover tooltips
ptrap_volcano(res, interactive = TRUE)
} # }