Per-point colours for a volcano plot — colour_volcano

Builds a named colour vector marking up/down-regulated (and optionally selected) genes, in the format expected by the point_colours argument of volcano_plot(). The names give each point's group and the values its colour.

Usage

colour_volcano_points(
  volcano.data,
  increase.col = "Red",
  decreased.col = "Blue",
  highlight.selected = FALSE,
  selected.cols = c("Green", "Orange"),
  highlight.genes = "NKG7",
  FDR.cutoff = 0.05,
  logFC.cutoff = 1
)

Arguments

volcano.data: Data frame with FDR and logFC, gene symbols as rownames.
increase.col, decreased.col: Colours for up/down-regulated genes.
highlight.selected: If TRUE, recolour the genes in highlight.genes.
selected.cols: Length-2 colours for selected up / down genes.
highlight.genes: Character vector of genes to highlight.
FDR.cutoff, logFC.cutoff: Significance thresholds.

Value

A named character vector of colours (one per row).

Examples

df <- data.frame(FDR = c(0.01, 0.5), logFC = c(2, 0),
                 row.names = c("NKG7", "B"))
colour_volcano_points(df)
#> Increased        NS 
#>     "Red"  "grey50"