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Geom for Hi-C contact matrix visualization (triangle/rotated view)

Source: R/geom_hic.R
geom_hic_triangle.Rd

This function creates a geom for Hi-C contact matrix visualization in a triangle (rotated 45-degree) view. This is the standard view for genome browser tracks where the x-axis shows genomic position and the y-axis shows interaction distance.

Usage

geom_hic_triangle(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  resolution = NULL,
  max_distance = NULL,
  na.rm = FALSE,
  rasterize = FALSE,
  rasterize_dpi = 300,
  show.legend = NA,
  inherit.aes = TRUE
)

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.

...

Additional arguments passed to ggplot2::layer()

resolution

Resolution of Hi-C bins in base pairs. Required for proper diamond sizing. If NULL, attempts to infer from data (default: NULL)

max_distance

Maximum interaction distance to display in base pairs (default: NULL, show all)

na.rm

If TRUE, silently remove missing values.

rasterize

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

rasterize_dpi

Resolution for rasterization in dots per inch. Default: 300

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().

Value

A ggplot2 layer that can be added to a plot.

Details

The triangle view transforms Hi-C data so that:

  • x-axis represents the midpoint of interacting bins: (pos1 + pos2) / 2

  • y-axis represents the interaction distance: pos2 - pos1

The triangle points UPWARD with the diagonal (self-interactions) at y=0 at the bottom, and the apex at the top showing maximum interaction distance. Each contact is rendered as a diamond (rotated square). Use with coord_fixed(ratio = 1) for a proper half-square aspect ratio where the triangle forms 45-degree edges.

Examples

if (FALSE) { # \dontrun{
library(ggplot2)
# Create example Hi-C data
hic_df <- expand.grid(
  pos1 = seq(1000000, 1500000, by = 10000),
  pos2 = seq(1000000, 1500000, by = 10000)
)
hic_df <- hic_df[hic_df$pos2 >= hic_df$pos1, ]  # Upper triangle only
hic_df$score <- runif(nrow(hic_df))

ggplot(hic_df, aes(x = pos1, y = pos2, fill = score)) +
  geom_hic_triangle(resolution = 10000) +
  scale_fill_hic() +
  coord_fixed(ratio = 1)

# With rasterization for large matrices
ggplot(hic_df, aes(x = pos1, y = pos2, fill = score)) +
  geom_hic_triangle(resolution = 10000, rasterize = TRUE) +
  scale_fill_hic() +
  coord_fixed(ratio = 1)
} # }