Apply an evidence-aware p-value color scale — scale_color

Maps raw p-values to either the Inferno or Viridis color palette using a threshold-aware transformation. The transformation allocates additional visual resolution around commonly interpreted p-value thresholds of 0.05, 0.01, and 0.001. Values above 0.05 are progressively desaturated to reduce their visual emphasis while retaining a continuous representation of the underlying p-values. The colorbar uses the same warped coordinates, so its raw p-value labels remain separated around these thresholds. Use this scale when p-values are mapped to the color aesthetic.

Usage

scale_color_pvalue(
  palette = "inferno",
  direction = -1,
  name = "P-value",
  breaks = c(1, 0.1, 0.05, 0.01, 0.001, 1e-05, 1e-08),
  labels = .format_pvalue_labels,
  limits = c(1e-08, 1),
  na.value = "grey80",
  guide = NULL,
  ...
)

Arguments

palette: A character value specifying the color palette. Must be "inferno" or "viridis". Defaults to "inferno".
direction: A numeric value controlling the direction of the palette. Use -1, the default, for darker colors to indicate smaller p-values and stronger statistical evidence. Use 1 to reverse the palette.
name: The legend title. Defaults to "P-value".
breaks: A numeric vector of raw p-values to display as legend breaks. Defaults to commonly interpreted statistical thresholds and reference values.
labels: A function or character vector used to label the legend breaks. By default, the legend displays raw p-values rather than transformed values.
limits: A numeric vector containing the minimum and maximum p-values represented by the scale. Values outside these limits are squished to the nearest limit. Defaults to c(1e-8, 1).
na.value: The color assigned to missing p-values. Defaults to "grey80".
guide: A guide function or guide name. The default, NULL, uses a taller colorbar so the threshold-aware breaks remain legible. Supply "colourbar" for ggplot2's standard-sized colorbar or another guide to override this behavior.
...: Additional arguments passed to ggplot2::continuous_scale().

Value

A continuous ggplot2 color scale.

Examples

# \donttest{
data(SampleData)
data(SampleVariableTypes)

Labelled <- RevalueData(SampleData, SampleVariableTypes)$RevaluedData

# Four outcomes by six predictors: 24 standardized associations.
screen <- MakeUnivariateRegressionTable(
  data = Labelled,
  outcome_vars = c("tau", "p_tau", "AXL", "Ferritin"),
  predictor_vars = c(
    "age", "sex", "Adiponectin", "Cortisol", "Insulin", "Leptin"
  ),
  Standardize = TRUE
)

# A volcano plot is the natural home for this scale: effect size on x,
# evidence on y, and the colour reinforcing where the thresholds fall so
# the eye is not left to judge distance along a log axis.
ggplot2::ggplot(
  screen$Results,
  ggplot2::aes(
    x = Estimate,
    y = -log10(PValue),
    color = PValue
  )
) +
  ggplot2::geom_point(size = 2.5) +
  ggplot2::geom_hline(yintercept = -log10(0.05), linetype = "dashed") +
  ggplot2::geom_vline(xintercept = 0, linetype = "dotted") +
  scale_color_pvalue() +
  ggplot2::labs(
    title = "Standardized associations across four outcomes",
    subtitle = "Dashed line: p = 0.05. Dotted line: no effect.",
    x = "Estimate per SD", y = expression(-log[10](p))
  ) +
  ggplot2::theme_bw()

# }