Add gene annotation tracks to Hi-C plots

Displays gene models as annotation tracks below Hi-C heatmaps, showing gene structure with exons, introns, UTRs, and strand orientation. Gene annotations are automatically retrieved from GTF files or TxDb objects and positioned below the Hi-C plot with gene symbols labeled underneath. The function supports two visualization styles: "basic" (detailed exon/intron structure) and "arrow" (simplified arrow representation indicating strand direction).

Usage

geom_annotation(
  mapping = NULL,
  data = NULL,
  stat = StatAnnotation,
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  txdb = NULL,
  tx2gene = NULL,
  gtf_path = NULL,
  width_ratio = 1/50,
  spacing_ratio = 1/3,
  maxgap = -1,
  include_ncrna = TRUE,
  style = c("basic", "arrow"),
  gene_symbols = NULL,
  chrom_prefix = TRUE,
  fontsize = 10,
  colour = "#48CFCB",
  fill = "#48CFCB",
  draw_boundary = TRUE,
  boundary_colour = "black",
  linetype = "dashed",
  ...
)

Arguments

mapping

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

stat

The statistical transformation to use on the data for this layer. When using a geom_*() function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

• A Stat ggproto subclass, for example StatCount.

• A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

• For more information and other ways to specify the stat, see the layer stat documentation.

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

• The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

• A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

• For more information and other ways to specify the position, see the layer position documentation.

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. annotation_borders().

txdb

A TxDb object from the GenomicFeatures package containing transcript annotations. Must be provided together with tx2gene if gtf_path is not specified. Default is NULL.

tx2gene

A data frame or tibble mapping transcript information to gene information. Required if using txdb parameter. Should include the following columns:

• chrom: Chromosome number or name

• gene_id: Entrez gene ID or unique gene identifier

• gene_symbol: Common gene symbol or name (e.g., "TP53", "BRCA1")

• tx_id: Entrez transcript ID or unique transcript identifier

• tx_name: Name of the transcript

• gene_type: Gene biotype (e.g., "protein_coding", "lncRNA")

• tx_type: Transcript biotype Default is NULL.

gtf_path

Character string specifying the path to a GTF/GFF file. The function will automatically parse the GTF file to generate txdb and tx2gene objects. Parsed data is cached to speed up subsequent calls. Either gtf_path or both txdb and tx2gene must be provided. Default is NULL.

width_ratio

Numeric value controlling the height of each gene track relative to the Hi-C plot height. Smaller values create thinner tracks. Default is 1/50 (2% of Hi-C plot height).

spacing_ratio

Numeric value controlling the vertical spacing between gene tracks as a proportion of track height. Larger values increase spacing. Default is 1/3 (33% of track height).

maxgap

Integer specifying the maximum genomic distance (in bp) between genes on the same horizontal line. Genes within this distance will be placed on separate lines to prevent overlap. Set to -1 for automatic spacing. Default is -1.

include_ncrna

Logical indicating whether to include non-coding RNA genes (lncRNA, miRNA, etc.) in the annotation track. Set to FALSE to show only protein-coding genes. Default is TRUE.

style

Character string specifying the visualization style. Options:

• "basic": Shows detailed gene structure with distinct exons (thick boxes), introns (thin lines with directional arrows), and UTRs (thin boxes)

• "arrow": Simplified representation showing each gene as a single arrow pointing in the direction of transcription (5' to 3') Default is "basic".

gene_symbols

Character vector of specific gene symbols to display. When provided, only these genes will be shown in the annotation track. Useful for highlighting genes of interest. Default is NULL (show all genes).

chrom_prefix

Logical indicating whether chromosome names include the "chr" prefix (e.g., "chr1" vs "1"). Should match the naming convention in your Hi-C data. Default is TRUE.

fontsize

Numeric value specifying the font size for gene symbol labels. Default is 10.

colour

Character string specifying the outline color for gene features. Default is "#48CFCB" (teal).

fill

Character string specifying the fill color for gene features (exons, UTRs, arrows). Default is "#48CFCB" (teal).

draw_boundary

Logical indicating whether to draw vertical boundary lines between chromosomes in multi-chromosome displays. Default is TRUE.

boundary_colour

Character string specifying the color of chromosome boundary lines. Default is "black".

linetype

Character string or integer specifying the line type for chromosome boundaries. Default is "dashed".

...

Additional parameters (currently ignored).

Value

A ggplot2 layer object that can be added to a gghic plot.

Details

Required Aesthetics

This geom inherits aesthetics from the Hi-C data and requires:

• seqnames1, seqnames2: Chromosome names

• start1, start2: Start positions

• end1, end2: End positions

Gene Annotation Sources

Gene annotations can be provided in three ways:

1. GTF file via gtf_path: Most convenient, automatically parsed and cached

2. TxDb + tx2gene: Pre-processed annotations for custom databases

3. Downloaded from online repositories (Ensembl, UCSC, GENCODE)

Visualization Styles

Basic Style (style = "basic")

Shows detailed gene structure:

• Coding exons (CDS): Thick rectangles in full color

• UTRs: Thinner rectangles showing 5' and 3' untranslated regions

• Introns: Thin lines with small directional arrows indicating strand

• ncRNAs: Thin rectangles for non-coding transcripts (if include_ncrna = TRUE)

Arrow Style (style = "arrow")

Simplified representation:

• Each gene shown as a single arrow shape

• Arrow points from 5' to 3' direction

• More compact, suitable for dense genomic regions

Gene Placement and Layout

• Genes are automatically arranged on multiple horizontal lines to prevent overlap

• Genes closer than maxgap are placed on separate lines

• Gene symbols are centered below each gene

• Multiple tracks are vertically stacked with spacing controlled by spacing_ratio

Multi-Chromosome Display

When displaying multiple chromosomes:

• Coordinates are automatically adjusted for proper alignment

• Vertical boundary lines separate chromosomes (if draw_boundary = TRUE)

• Gene labels maintain proper positioning across chromosome boundaries

Gene Filtering

Use gene_symbols parameter to highlight specific genes:

• Provide a character vector of gene names

• Only matching genes will be displayed

• Useful for focusing on candidate genes or pathways

Performance Considerations

• GTF parsing is cached for faster subsequent loading

• For large genomic regions, consider filtering genes with gene_symbols

• Setting include_ncrna = FALSE reduces the number of features

• Arrow style renders faster than basic style for dense regions

See also

• gghic() for creating the base Hi-C plot

• geom_hic() for the Hi-C heatmap layer

• geom_track() and geom_track2() for genomic signal tracks

• geom_ideogram() for chromosome ideograms

Examples

if (FALSE) { # \dontrun{
# Basic usage with GTF file
cc <- ChromatinContacts("path/to/cooler.cool", focus = "chr4") |>
  import()

gtf_file <- "path/to/genes.gtf"
gghic(cc) + geom_annotation(gtf_path = gtf_file)

# Filter specific genes of interest
gghic(cc) +
  geom_annotation(
    gtf_path = gtf_file,
    gene_symbols = c("BRCA1", "TP53", "MYC")
  )

# Arrow style with custom colors
gghic(cc) +
  geom_annotation(
    gtf_path = gtf_file,
    style = "arrow",
    colour = "darkblue",
    fill = "lightblue",
    fontsize = 8
  )

# Exclude non-coding RNAs for cleaner view
gghic(cc) +
  geom_annotation(
    gtf_path = gtf_file,
    include_ncrna = FALSE
  )

# Custom track dimensions
gghic(cc) +
  geom_annotation(
    gtf_path = gtf_file,
    width_ratio = 1 / 40,    # Taller tracks
    spacing_ratio = 1 / 2     # More spacing
  )

# Using TxDb object directly
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
tx2gene <- read.csv("tx2gene_mapping.csv")

gghic(cc) +
  geom_annotation(txdb = txdb, tx2gene = tx2gene)

# Multiple genes with custom styling
candidates <- c("PDGFRA", "KIT", "KDR", "FLT1")
gghic(cc) +
  geom_annotation(
    gtf_path = gtf_file,
    gene_symbols = candidates,
    colour = "red",
    fill = "pink",
    fontsize = 12
  )

# Without chromosome prefix (e.g., "1" instead of "chr1")
gghic(cc) +
  geom_annotation(
    gtf_path = gtf_file,
    chrom_prefix = FALSE
  )

# Multi-chromosome with boundaries
cc_multi <- ChromatinContacts("path/to/cooler.cool",
                              focus = c("chr4", "chr8")) |>
  import()
gghic(cc_multi) +
  geom_annotation(
    gtf_path = gtf_file,
    draw_boundary = TRUE,
    boundary_colour = "gray50",
    linetype = "dotted"
  )

# Protein-coding genes only with arrow style
gghic(cc) +
  geom_annotation(
    gtf_path = gtf_file,
    include_ncrna = FALSE,
    style = "arrow",
    fill = "#2E86AB"
  )
} # }