Visualize TAD boundaries on Hi-C heatmap

Adds topologically associating domain (TAD) boundary annotations to Hi-C contact maps. TAD boundaries are displayed as triangular outlines marking the diagonal extent of each domain.

Usage

geom_tad(
  mapping = NULL,
  data = NULL,
  stat = StatTad,
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  tad_path = NULL,
  tad_gis = NULL,
  is_0_based = FALSE,
  colour = "grey",
  ...
)

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().

tad_path

Character. Path to BED-like file with TAD coordinates (columns: chrom, start, end). Either tad_path or tad_gis must be provided (default: NULL).

tad_gis

GInteractions object containing TAD coordinates as interactions from start to end positions. Either tad_path or tad_gis must be provided (default: NULL).

is_0_based

Logical. Whether input coordinates are 0-based (BED format). Set TRUE for BED files (default: FALSE).

colour

Character. Color for TAD boundary lines (default: "grey").

...

Additional parameters passed to layer (unused).

Value

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

Details

Required aesthetics

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

TAD file format

Tab-delimited BED-like file with columns:

chrom  start     end
chr1   0         1000000
chr1   1000000   2500000

Interpretation

TAD boundaries are drawn as V-shaped lines on the Hi-C diagonal. Each TAD is represented by two lines forming a triangle that encloses the domain. Darker regions inside triangles represent increased intra-TAD interactions.

Examples

if (FALSE) { # \dontrun{
# Basic usage with TAD file
cc <- ChromatinContacts("file.cool", focus = "chr4") |> import()
gghic(cc) + geom_tad(tad_path = "tads.bed")

# Custom color
gghic(cc) + geom_tad(tad_path = "tads.bed", colour = "blue")

# Using GInteractions object
tads <- rtracklayer::import("tads.bed") |> as("GInteractions")
gghic(cc) + geom_tad(tad_gis = tads)

# 0-based coordinates (BED format)
gghic(cc) + geom_tad(tad_path = "tads.bed", is_0_based = TRUE)

# Combined with loops
gghic(cc) +
  geom_tad(tad_path = "tads.bed", colour = "grey") +
  geom_loop(loop_path = "loops.bedpe", colour = "red")
} # }