Create Hi-C visualization plot

High-level wrapper for publication-ready Hi-C visualizations with genomic features.

Usage

gghic(x, ...)

# S4 method for class 'ChromatinContacts'
gghic(
  x,
  scale_method = log10,
  ideogram = FALSE,
  ideogram_width_ratio = 1/30,
  ideogram_fontsize = 10,
  ideogram_colour = "red",
  ideogram_fill = "#FFE3E680",
  annotation = FALSE,
  annotation_style = "basic",
  annotation_width_ratio = 1/50,
  annotation_spacing_ratio = 1/3,
  annotation_fontsize = 10,
  annotation_colour = "#48CFCB",
  annotation_fill = "#48CFCB",
  track = FALSE,
  track_width_ratio = 1/20,
  track_spacing_ratio = 1/2,
  track_fill = "black",
  track_fontsize = 5,
  tad = FALSE,
  tad_colour = "grey",
  loop = FALSE,
  loop_style = "circle",
  loop_colour = "black",
  loop_fill = NA,
  concatemer = FALSE,
  concatemer_width_ratio = 1/100,
  concatemer_spacing_ratio = 1/5,
  expand_xaxis = FALSE,
  expand_left = NULL,
  expand_right = NULL,
  ...
)

# S4 method for class 'data.frame'
gghic(
  x,
  scale_column = "balanced",
  scale_method = log10,
  ideogram = FALSE,
  ideogram_width_ratio = 1/30,
  ideogram_fontsize = 10,
  ideogram_colour = "red",
  ideogram_fill = "#FFE3E680",
  annotation = FALSE,
  annotation_style = "basic",
  annotation_width_ratio = 1/50,
  annotation_spacing_ratio = 1/3,
  annotation_fontsize = 10,
  annotation_colour = "#48CFCB",
  annotation_fill = "#48CFCB",
  track = FALSE,
  track_width_ratio = 1/20,
  track_spacing_ratio = 1/2,
  track_fill = "black",
  track_fontsize = 5,
  tad = FALSE,
  tad_is_0_based = FALSE,
  tad_colour = "grey",
  loop = FALSE,
  loop_style = "circle",
  loop_is_0_based = FALSE,
  loop_colour = "black",
  loop_fill = NA,
  concatemer = FALSE,
  concatemer_width_ratio = 1/100,
  concatemer_spacing_ratio = 1/5,
  expand_xaxis = FALSE,
  expand_left = NULL,
  expand_right = NULL,
  ...
)

# S4 method for class 'GInteractions'
gghic(
  x,
  scale_column = "balanced",
  scale_method = log10,
  ideogram = FALSE,
  ideogram_width_ratio = 1/30,
  ideogram_fontsize = 10,
  ideogram_colour = "red",
  ideogram_fill = "#FFE3E680",
  annotation = FALSE,
  annotation_style = "basic",
  annotation_width_ratio = 1/50,
  annotation_spacing_ratio = 1/3,
  annotation_fontsize = 10,
  annotation_colour = "#48CFCB",
  annotation_fill = "#48CFCB",
  track = FALSE,
  track_width_ratio = 1/20,
  track_spacing_ratio = 1/2,
  track_fill = "black",
  track_fontsize = 5,
  tad = FALSE,
  tad_is_0_based = FALSE,
  tad_colour = "grey",
  loop = FALSE,
  loop_style = "circle",
  loop_is_0_based = FALSE,
  loop_colour = "black",
  loop_fill = NA,
  concatemer = FALSE,
  concatemer_width_ratio = 1/100,
  concatemer_spacing_ratio = 1/5,
  expand_xaxis = FALSE,
  expand_left = NULL,
  expand_right = NULL,
  ...
)

Arguments

x: ChromatinContacts, GInteractions, or data.frame with interactions.
...: Additional arguments for geom functions.
scale_method: Function for data transformation (default: log10).
ideogram: Logical. Add chromosome ideogram (default: FALSE).
ideogram_width_ratio: Numeric. Ideogram height ratio (default: 1/30).
ideogram_fontsize: Numeric. Ideogram font size (default: 10).
ideogram_colour: Character. Highlight color (default: "red").
ideogram_fill: Character. Highlight fill (default: "#FFE3E680").
annotation: Logical. Add gene annotations (default: FALSE). Requires gtf_path in ....
annotation_style: Character. "basic" or "arrow" (default: "basic").
annotation_width_ratio: Numeric. Track height (default: 1/50).
annotation_spacing_ratio: Numeric. Gene spacing (default: 1/3).
annotation_fontsize: Numeric. Label size (default: 10).
annotation_colour: Character. Feature color (default: "#48CFCB").
annotation_fill: Character. Feature fill (default: "#48CFCB").
track: Logical. Add genomic tracks (default: FALSE). Requires tracks in object or data_paths in ....
track_width_ratio: Numeric. Track height (default: 1/20).
track_spacing_ratio: Numeric. Track spacing (default: 1/2).
track_fill: Character. Track colors (default: "black").
track_fontsize: Numeric. Label size (default: 5).
tad: Logical. Add TAD boundaries (default: FALSE). Requires TADs in object or tad_path in ....
tad_colour: Character. TAD color (default: "grey").
loop: Logical. Add loops (default: FALSE). Requires loops in object or loop_path in ....
loop_style: Character. "circle" or "arc" (default: "circle").
loop_colour: Character. Loop color (default: "black").
loop_fill: Fill color (default: NA).
concatemer: Logical. Add multi-way contacts (default: FALSE).
concatemer_width_ratio: Numeric. Track height (default: 1/100).
concatemer_spacing_ratio: Numeric. Spacing (default: 1/5).
expand_xaxis: Logical. Expand x-axis (default: FALSE).
expand_left: Numeric. Left expansion in bp (default: 10×resolution).
expand_right: Numeric. Right expansion in bp (default: 10×resolution).
scale_column: Character string. Name of the column to use for scaling (e.g., "balanced", "count"). Used when input is GInteractions or data.frame.
tad_is_0_based: Logical. Whether TAD coordinates are 0-based. Default is TRUE.
loop_is_0_based: Logical. Whether loop coordinates are 0-based. Default is TRUE.

Value

ggplot2 object.

Details

Automatically handles: data scaling, coordinate transformation, feature integration, axis labels, default theme.

Use individual geom_*() functions for more control: geom_hic(), geom_ideogram(), geom_annotation(), geom_track(), geom_tad(), geom_loop(), geom_concatemer().

Examples

if (FALSE) { # \dontrun{
# Basic usage
cc <- ChromatinContacts("file.cool") |> import()
gghic(cc)
gghic(cc["chr4:0-50000000"])

# With features
gghic(cc, ideogram = TRUE, genome = "hg19")
gghic(cc, tad = TRUE, tad_path = "tads.bed")
gghic(cc, loop = TRUE, loop_path = "loops.bedpe")

# With tracks
features(cc, "tracks") <- GRangesList(
  H3K27ac = rtracklayer::import("track.bw")
)
gghic(cc, track = TRUE, track_fill = "blue")
} # }