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Easy Hi-C track visualization

Source: R/geom_hic.R
ez_hic.Rd

This function creates a Hi-C contact matrix visualization from various input types. It provides a high-level interface supporting both square heatmap and triangle (rotated) views commonly used in genome browsers.

Usage

ez_hic(
  data,
  region,
  resolution = 10000,
  style = c("triangle", "square"),
  palette = c("cooler", "ylgnbu", "viridis", "bwr"),
  trans = "log10",
  limits = NULL,
  max_distance = NULL,
  rasterize = FALSE,
  show_diagonal = TRUE,
  ...
)

Arguments

data

Input data. Can be:

  • A matrix: Dense contact matrix

  • A data frame: Sparse format with (pos1, pos2, score) or (bin1, bin2, score)

  • A file path: Tab-delimited matrix file

region

Genomic region to display (e.g., "chr1:1000000-2000000")

resolution

Resolution of the Hi-C data in base pairs (default: 10000)

style

Visualization style: "triangle" (default, rotated view) or "square"

palette

Color palette: "cooler" (red, default), "ylgnbu", "viridis", or "bwr"

trans

Scale transformation: "identity" (linear), "log10" (default), "log2", "sqrt"

limits

Numeric vector of length 2 for color scale limits (default: NULL, auto)

max_distance

Maximum interaction distance to show in base pairs (default: NULL, show all). Only applies to triangle style.

rasterize

Logical. If TRUE and ggrastr package is available, rasterize the plot for better performance with large matrices. Default: FALSE

show_diagonal

Logical. If TRUE, show the diagonal (self-interactions). Default: TRUE

...

Additional arguments passed to geom_hic or geom_hic_triangle

Value

A ggplot2 object

Examples

if (FALSE) { # \dontrun{
# Create example data
mat <- matrix(runif(2500), nrow = 50)
mat <- mat + t(mat)  # Make symmetric
diag(mat) <- diag(mat) * 2  # Stronger diagonal

# Triangle view (default)
ez_hic(mat, "chr1:1000000-1500000", resolution = 10000)

# Square heatmap view
ez_hic(mat, "chr1:1000000-1500000", resolution = 10000, style = "square")

# With log10 transformation and custom palette
ez_hic(mat, "chr1:1000000-1500000",
  resolution = 10000,
  trans = "log10",
  palette = "ylgnbu"
)

# Limit maximum distance shown
ez_hic(mat, "chr1:1000000-1500000",
  resolution = 10000,
  max_distance = 200000
)
} # }