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Visualize inverted Hi-C heatmap below main contact map

Source: R/geom-hic-under.R
geom_hic_under.Rd

Creates a flipped (inverted) Hi-C contact heatmap positioned below the main plot. Useful for comparing two datasets or showing the same data with different color scales/transformations.

Usage

geom_hic_under(
  mapping = NULL,
  data = NULL,
  stat = StatHicUnder,
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  rasterize = TRUE,
  dpi = 300,
  dev = "cairo",
  scale = 1,
  draw_boundary = TRUE,
  boundary_colour = "black",
  linetype = "dashed",
  ...
)

Arguments

mapping

Set of aesthetic mappings created by ggplot2::aes(). Must include fill aesthetic.

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().

rasterize

Logical. Rasterize for performance (default: TRUE).

dpi

Numeric. Rasterization resolution (default: 300).

dev

Character. Graphics device for rasterization (default: "cairo").

scale

Numeric. Rasterization scaling factor (default: 1).

draw_boundary

Logical. Draw chromosome boundaries for multi-chromosome plots (default: TRUE).

boundary_colour

Character. Boundary line color (default: "black").

linetype

Boundary line type (default: "dashed").

...

Additional parameters (unused).

Value

A ggplot2 layer for the inverted Hi-C heatmap.

Details

Required aesthetics

  • seqnames1, start1, end1: First anchor coordinates

  • seqnames2, start2, end2: Second anchor coordinates

  • fill: Color scale values

Usage

This geom requires a main Hi-C plot created with geom_hic() first. The inverted heatmap is automatically positioned below, using independent color scales via fill2 aesthetic.

Common use cases

  • Compare two experimental conditions

  • Show raw vs. normalized data

  • Display same data with different color scales

See also

geom_hic(), gghic(), renameGeomAes()

Examples

if (FALSE) { # \dontrun{
# Compare two datasets
cc1 <- ChromatinContacts("sample1.cool") |> import()
cc2 <- ChromatinContacts("sample2.cool") |> import()

library(ggplot2)
ggplot() +
  geom_hic(data = scaleData(cc1, "balanced", log10),
           aes(seqnames1 = seqnames1, start1 = start1, end1 = end1,
               seqnames2 = seqnames2, start2 = start2, end2 = end2,
               fill = score)) +
  geom_hic_under(data = scaleData(cc2, "balanced", log10),
                 aes(seqnames1 = seqnames1, start1 = start1, end1 = end1,
                     seqnames2 = seqnames2, start2 = start2, end2 = end2,
                     fill2 = score)) +
  scale_fill_viridis_c() +
  scale_fill2_viridis_c(option = "magma")
# Load two Hi-C datasets for comparison
cc1 <- ChromatinContacts("path/to/cooler.cool", focus = "chr4") |>
  import()

# Simulate a second dataset (in practice, load a different sample)
cc2 <- cc1

# Compare two Hi-C maps with different color scales
library(ggplot2)
ggplot() +
  geom_hic(
    data = scaleData(cc1, "balanced", log10),
    aes(
      seqnames1 = seqnames1, start1 = start1, end1 = end1,
      seqnames2 = seqnames2, start2 = start2, end2 = end2, fill = score
    )
  ) +
  geom_hic_under(
    data = scaleData(cc2, "balanced", log10),
    aes(
      seqnames1 = seqnames1, start1 = start1, end1 = end1,
      seqnames2 = seqnames2, start2 = start2, end2 = end2, fill2 = score
    )
  ) |>
  renameGeomAes(new_aes = c("fiil" = "fill2")) +
  scale_fill_gradientn(
    aesthetics = "fill2", colors = c("white", "blue"), name = "Sample 2"
  ) +
  theme_hic()
} # }