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Visualize chromatin loops on Hi-C heatmap

Source: R/geom-loop.R
geom_loop.Rd

Adds chromatin loop annotations to Hi-C contact maps. Loops can be displayed as circles (points) or arcs. Automatically filters loops to display only those within the plotted region.

Usage

geom_loop(
  mapping = NULL,
  data = NULL,
  stat = StatLoop,
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  loop_path = NULL,
  loop_gis = NULL,
  is_0_based = FALSE,
  style = "circle",
  n_arc_points = 50,
  colour = "black",
  shape = 21,
  fill = NA,
  size = grid::unit(1/80, "native"),
  stroke = 1,
  ...
)

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().

loop_path

Character. Path to loop file in BEDPE-like format with columns: chrom1, start1, end1, chrom2, start2, end2. Either loop_path or loop_gis must be provided (default: NULL).

loop_gis

GInteractions object containing loop coordinates. Either loop_path or loop_gis must be provided (default: NULL).

is_0_based

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

style

Character. Visualization style:

  • "circle": display loops as circular points (default)

  • "arc": display loops as curved arcs connecting anchors

n_arc_points

Integer. Number of points used to draw each arc when style = "arc". Higher values produce smoother curves (default: 50).

colour

Character. Color for loop markers or arcs (default: "black").

shape

Integer. Point shape when style = "circle" (default: 21 = filled circle).

fill

Character. Fill color for points when style = "circle" (default: NA for transparent).

size

Unit or numeric. Size of loop markers. Can be a grid unit or numeric value in mm (default: unit(1/80, "native")).

stroke

Numeric. Line width for point borders or arc lines (default: 1).

...

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

Loop file format

Tab-delimited file with columns:

chrom1  start1  end1  chrom2  start2  end2
chr1    1000000 1005000 chr1  2000000 2005000

Performance tips

For large loop files, pre-filter to region of interest before plotting. Arc style is more computationally intensive than circle style.

See also

geom_tad() for TAD boundaries, gghic() for creating Hi-C plots

Examples

if (FALSE) { # \dontrun{
# Basic usage with loop file
cc <- ChromatinContacts("file.cool", focus = "chr4") |> import()
gghic(cc) + geom_loop(loop_path = "loops.bedpe")

# Arc style visualization
gghic(cc) + 
  geom_loop(loop_path = "loops.bedpe", style = "arc", colour = "red")

# Using GInteractions object
loops <- rtracklayer::import("loops.bedpe")
gghic(cc) + geom_loop(loop_gis = loops, colour = "blue", size = 2)

# 0-based coordinates (BEDPE format)
gghic(cc) + geom_loop(loop_path = "loops.bedpe", is_0_based = TRUE)

# Customized appearance
gghic(cc) +
  geom_loop(
    loop_path = "loops.bedpe",
    colour = "darkred",
    fill = "red",
    size = 3,
    stroke = 1.5,
    shape = 21
  )
} # }