Position scales for genomic data (x & y)

scale_x_genomic() and scale_y_genomic() are the default scales for x and y aesthetics defined as representations of genomic positions such as GPos and GRanges (sub)-classes.

scale_x_genomic(
  name = waiver(),
  breaks = waiver(),
  minor_breaks = waiver(),
  n.breaks = NULL,
  labels = waiver(),
  minor_labels = waiver(),
  limits = NULL,
  expand = waiver(),
  oob = censorThis,
  na.value = NA_real_,
  trans = S4TransIdentity,
  guide = "genomic_axis",
  position = "bottom",
  sec.axis = waiver()
)

scale_y_genomic(
  name = waiver(),
  breaks = waiver(),
  minor_breaks = waiver(),
  n.breaks = NULL,
  labels = waiver(),
  minor_labels = waiver(),
  limits = NULL,
  expand = waiver(),
  oob = censorThis,
  na.value = NA_real_,
  trans = S4TransIdentity,
  guide = "genomic_axis",
  position = "left",
  sec.axis = waiver()
)

Arguments

name	The name of the scale. Used as the axis or legend title. If `waiver()`, the default, the name of the scale is taken from the first mapping used for that aesthetic. If `NULL`, the legend title will be omitted.
breaks	One of: `NULL` for no breaks `waiver()` for the default breaks computed by the transformation object. A `GPos` object of positions. A function that takes the `GRanges` limits and returns `GPos` breaks as output.
minor_breaks	One of: `NULL` for no minor breaks `waiver()` for the default minor breaks. A `GPos` object of positions. A function that takes the `GRanges` limits and returns `GPos` minor breaks as output.
n.breaks	An integer guiding the number of major breaks. The algorithm may choose a slightly different number to ensure nice break labels. Will only have an effect if `breaks = waiver()`. Use `NULL` to use the default number of breaks given by the transformation.
labels	One of: `NULL` for no labels `waiver()` for the default labels computed by the transformation object A character vector giving labels (must be same length as `breaks`) A function that takes the breaks as input and returns labels as output
minor_labels	One of: `NULL` for no minor labels. `waiver()` for the default labels computed by the transformation object. A `character` vector giving labels (must be same length as `minor_breaks`.) A `function` that takes the minor breaks as input and returns labels as output. Keep in mind that displaying the minor labels is dependent on wether the `guide` supports this and the default `guide_axis()` does not.
limits	One of: `NULL` to use the default scale range . A `GRanges` object with at most one range per seqlevel to be displayed. A function that accepts the existing (automatic) limits as `GRanges` object and returns the new limits as a `GRanges` object. Note that by default, setting limits on positional scales will remove data outside of the limits. Change the `oob` argument to change this behaviour.
expand	For position scales, a vector of range expansion constants used to add some padding around the data to ensure that they are placed some distance away from the axes. Use the convenience function `expansion()` to generate the values for the `expand` argument. The defaults are to expand the scale by 5% on each side for continuous variables, and by 0.6 units on each side for discrete variables.
oob	One of: Function that handles limits outside of the scale limits (out of bounds). The default (`scales::censor()`) replaces out of bounds values with `NA`. `scales::squish()` for squishing out of bounds values into range. `scales::squish_infinite()` for squishing infinite values into range.
na.value	Missing values will be replaced with this value.
trans	For continuous scales, the name of a transformation object or the object itself. Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time". A transformation object bundles together a transform, its inverse, and methods for generating breaks and labels. Transformation objects are defined in the scales package, and are called `<name>_trans` (e.g., `scales::boxcox_trans()`). You can create your own transformation with `scales::trans_new()`.
guide	A function used to create a guide or its name. See `guides()` for more information.
position	For position scales, The position of the axis. `left` or `right` for y axes, `top` or `bottom` for x axes.
sec.axis	`sec_axis()` is used to specify a secondary axis.

Value

A ScaleS4 ggproto object.

Details

It is important to note that the scale operates in genomic space when limits are defined as or inferred to be of the GRanges class. This has the following known consequences:

Data represented by unclassed numerical values can not be used on this scale.
The scale limits and breaks are represented by GRanges and GPos objects.

Furthermore, scale expansions as set through the expand argument, expand the scale limits per individual seqlevel.

Examples

require(GenomicRanges)

df <- DataFrame(
  x = GRanges(c("chr1:1000-2000", "chr1:1500-2500",
                "chr2:3000-4000", "chr3:4000-4500")),
  y = c(1, 2, 3, 2)
)

# The default scale for GenomicRanges is scale_(x|y)_genomic()
g <- ggplot(df, aes(xmin = x, xmax = x,
                    ymin = y - 0.2, ymax = y + 0.2)) +
  geom_rect()
g

# Major labels are parallel to the seqnames
g + scale_x_genomic(labels = LETTERS[1:3])

# Minor breaks are positional and specified with GPos or 1-width GRanges
g + scale_x_genomic(
  minor_breaks =  GPos(c("chr1:2000", "chr2:3500", "chr3:4000"))
)

# Minor breaks can also be labelled
g + scale_x_genomic(
  minor_breaks =  GPos(c("chr1:2000", "chr2:3500", "chr3:4000")),
  minor_labels = LETTERS[1:3]
)

Arguments

Value

Details

See also

Examples