Scale for Hi-C contact matrix fill colors — scale_fill

This function creates a continuous fill scale optimized for Hi-C contact matrix visualization. It provides common color palettes and supports log transformations.

Usage

scale_fill_hic(
  palette = c("cooler", "ylgnbu", "viridis", "bwr"),
  trans = "identity",
  limits = NULL,
  na.value = "grey50",
  midpoint = 0,
  oob = scales::squish,
  ...
)

Arguments

palette: Character string specifying the color palette. Options: "cooler" (red gradient, default), "ylgnbu" (yellow-green-blue), "viridis", or "bwr" (blue-white-red for diverging data)
trans: Transformation for the scale. Options: "identity" (linear, default), "log10", "log2", "sqrt". Can also pass a transformation object.
limits: Numeric vector of length 2 giving the scale limits. Values outside this range will be squished to the nearest limit. Default: NULL (auto)
na.value: Color for missing values (default: "grey50")
midpoint: For diverging palettes ("bwr"), the midpoint value (default: 0)
oob: Function to handle out-of-bounds values. Default: scales::squish
...: Additional arguments passed to ggplot2::scale_fill_gradientn or scale_fill_gradient2

Value

A ggplot2 scale object

Examples

if (FALSE) { # \dontrun{
library(ggplot2)
# Basic usage with default cooler palette
ggplot(hic_data, aes(x = x, y = y, fill = score)) +
  geom_hic() +
  scale_fill_hic()

# Log10 transformation
ggplot(hic_data, aes(x = x, y = y, fill = score)) +
  geom_hic() +
  scale_fill_hic(trans = "log10")

# Different palette with limits
ggplot(hic_data, aes(x = x, y = y, fill = score)) +
  geom_hic() +
  scale_fill_hic(palette = "ylgnbu", limits = c(0, 100))

# Diverging palette for comparison data
ggplot(diff_data, aes(x = x, y = y, fill = log2fc)) +
  geom_hic() +
  scale_fill_hic(palette = "bwr", midpoint = 0)
} # }