Skip to contents

ggplot2 theme optimized for Hi-C contact maps

Source: R/theme-hic.R
theme_hic.Rd

Creates a clean, publication-ready theme for Hi-C visualization with optimized defaults: hidden y-axis, fixed coordinate ratio, and custom color gradient. Provides fine control over axis formatting and limits.

Usage

theme_hic(
  hide_y = TRUE,
  coord_ratio = 1,
  scale_fill_gradientn = TRUE,
  breaks = ggplot2::waiver(),
  labels = scales::unit_format(unit = "M", scale = 1e-06),
  xmin = NULL,
  xmax = NULL,
  expand_x = c(0, 0)
)

Arguments

hide_y

Logical. Hide y-axis elements (axis title, text, ticks) (default: TRUE). Y-axis typically uninformative for Hi-C plots.

coord_ratio

Numeric. Aspect ratio for ggplot2::coord_fixed(). 1 maintains equal x/y scaling (default: 1).

scale_fill_gradientn

Logical. Apply custom Hi-C color gradient (white → yellow → orange → red → black) (default: TRUE). Set FALSE to use custom scales.

breaks

Numeric vector or ggplot2::waiver(). X-axis break positions for ggplot2::scale_x_continuous(). Default uses automatic breaks.

labels

Function or character vector. X-axis label formatter. Default displays genomic coordinates in megabases (e.g., "10M" for 10,000,000 bp).

xmin

Numeric or NULL. Minimum x-axis limit. If NULL, uses data range (default: NULL).

xmax

Numeric or NULL. Maximum x-axis limit. If NULL, uses data range (default: NULL).

expand_x

Numeric vector (length 2). X-axis expansion in plot units: c(left_expansion, right_expansion) (default: c(0, 0) for no expansion).

Value

List of ggplot2 theme elements and scales that can be added to a ggplot object.

Details

Theme components

  • Based on theme_bw() with minimal grid lines

  • Hidden y-axis (configurable)

  • Fixed 1:1 coordinate ratio for accurate distance representation

  • Custom color gradient optimized for Hi-C data

  • Genomic coordinate formatting (Mb units)

Color gradient

The default gradient transitions through 13 colors from white (no contacts) to black (maximum contacts), providing excellent dynamic range for typical Hi-C data.

Customization

Combine with other ggplot2 theme elements for additional customization:

gghic(cc) + theme_hic() + theme(text = element_text(size = 14))

See also

gghic(), geom_hic(), ggplot2::theme()

Examples

if (FALSE) { # \dontrun{
cc <- ChromatinContacts("file.cool", focus = "chr4") |> import()

# Basic usage with default theme
gghic(cc) + theme_hic()

# Custom color scale
gghic(cc) +
  theme_hic(scale_fill_gradientn = FALSE) +
  scale_fill_viridis_c()

# Show y-axis
gghic(cc) + theme_hic(hide_y = FALSE)

# Custom axis limits and breaks
gghic(cc) +
  theme_hic(
    xmin = 1e6,
    xmax = 5e6,
    breaks = seq(1e6, 5e6, by = 1e6)
  )

# Custom axis labels (show kb instead of Mb)
gghic(cc) +
  theme_hic(labels = scales::unit_format(unit = "kb", scale = 1e-3))
} # }