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Add chromosome ideogram annotation to Hi-C plot

Source: R/geom-ideogram.R
geom_ideogram.Rd

Displays chromosome ideograms (cytogenetic band representations) above the Hi-C contact map, showing the genomic context with Giemsa staining patterns and highlighting the displayed region. Ideograms provide visual reference for chromosome structure, centromeres, and cytogenetic landmarks.

Usage

geom_ideogram(
  mapping = NULL,
  data = NULL,
  stat = StatIdeogram,
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  genome = "hg19",
  chrom_prefix = TRUE,
  highlight = TRUE,
  show_coord = FALSE,
  width_ratio = 1/30,
  length_ratio = 0.8,
  fontsize = 10,
  colour = "red",
  fill = "#FFE3E680",
  ...
)

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().

genome

Character. Genome assembly version for retrieving cytogenetic band information from UCSC. Supported genomes include:

  • "hg38": Human (GRCh38/hg38)

  • "hg19": Human (GRCh37/hg19) (default)

  • "mm10": Mouse (GRCm38)

  • "mm39": Mouse (GRCm39)

  • Other UCSC genome assemblies with cytoBand tables

chrom_prefix

Logical. Whether chromosome names in the data include "chr" prefix (e.g., "chr1" vs "1"). Set FALSE for Ensembl-style naming (default: TRUE).

highlight

Logical. Draw a colored outline around the displayed genomic region on the ideogram to emphasize the Hi-C map extent (default: TRUE).

show_coord

Logical. Display genomic coordinates (start-end) next to chromosome names on the ideogram (default: FALSE). Useful for showing exact region boundaries.

width_ratio

Numeric. Height of ideogram relative to Hi-C plot height (default: 1/30). Larger values create taller ideograms.

length_ratio

Numeric. Fraction of Hi-C plot width used for ideogram length (default: 0.8 = 80%). Controls horizontal scaling to leave space for labels.

fontsize

Numeric. Font size in points for chromosome labels and coordinates (default: 10).

colour

Character. Border color for the highlighted region box (default: "red").

fill

Character. Fill color for the highlighted region box, using RGBA hex format for transparency (default: "#FFE3E680" = semi-transparent light red).

...

Additional parameters (unused).

Value

A ggplot2 layer that can be added to a Hi-C plot.

Details

Required aesthetics

Inherits from Hi-C data: seqnames1, start1, end1, seqnames2, start2, end2

Ideogram structure

Chromosomes are displayed horizontally above the Hi-C map with:

  • Cytogenetic bands: Giemsa staining patterns (G-bands) shown with standard colors (light/dark representing staining intensity)

  • Centromeres: Typically appear as darker bands near the middle

  • Highlighted region: Colored box showing the exact genomic region displayed in the Hi-C map below

  • Labels: Chromosome names or coordinates on the right side

Multi-chromosome display

When visualizing multiple chromosomes, ideograms are stacked vertically in the same order as they appear in the Hi-C plot.

Genome assembly selection

Ensure the genome parameter matches your data's assembly. Mismatched assemblies will show incorrect cytogenetic band patterns or fail to retrieve band data.

Performance considerations

Ideogram data is fetched from UCSC Genome Browser on first use per session. Subsequent calls use cached data for improved performance.

See also

gghic(), geom_annotation(), geom_hic()

Examples

if (FALSE) { # \dontrun{
# Basic usage with human genome (hg19)
cc <- ChromatinContacts("sample.cool", focus = "chr4") |> import()
gghic(cc) + geom_ideogram(genome = "hg19")

# Use human GRCh38/hg38 assembly
gghic(cc) + geom_ideogram(genome = "hg38")

# Mouse genome
cc_mouse <- ChromatinContacts("mouse.cool", focus = "chr1") |> import()
gghic(cc_mouse) + geom_ideogram(genome = "mm10")

# Show coordinates instead of just chromosome names
gghic(cc) +
  geom_ideogram(genome = "hg19", show_coord = TRUE)

# Customize highlight colors
gghic(cc) +
  geom_ideogram(
    genome = "hg19",
    highlight = TRUE,
    colour = "blue",
    fill = "#ADD8E680"  # Semi-transparent light blue
  )

# Adjust ideogram size
gghic(cc) +
  geom_ideogram(
    genome = "hg19",
    width_ratio = 1/20,    # Taller ideogram
    length_ratio = 0.9,    # Wider ideogram
    fontsize = 12          # Larger labels
  )

# Multiple chromosomes with ideograms
cc_multi <- ChromatinContacts("sample.cool", focus = "chr1|chr2") |>
  import()
gghic(cc_multi) +
  geom_ideogram(genome = "hg19", show_coord = TRUE)

# Ensembl-style chromosome names (without "chr" prefix)
cc_ensembl <- ChromatinContacts("ensembl.cool", focus = "1") |> import()
gghic(cc_ensembl) +
  geom_ideogram(genome = "hg19", chrom_prefix = FALSE)

# Disable highlighting for cleaner look
gghic(cc) +
  geom_ideogram(genome = "hg19", highlight = FALSE)

# Complete publication-ready plot
gghic(cc, ideogram = FALSE) +  # Disable auto-ideogram
  geom_ideogram(
    genome = "hg19",
    highlight = TRUE,
    colour = "darkred",
    fill = "#FFE3E650",
    fontsize = 11
  ) +
  theme_hic()
} # }