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Genomic scales and base-pair labels

Source: R/scale_x_genomic.R
scale_x_genomic.Rd

Format genomic positions and scales using human-readable base-pair units. scale_x_genomic() is the default genomic x-axis scale for gggenomes plots. It wraps ggplot2::scale_x_continuous() with guide_scalebar() as its default guide. See axis_scalebar() for convenient configuration and styling of the scalebar. format_bp() formats numbers as base-pair quantities, and powers label_bp(), the default scale_x_genomic() labelling function.

Usage

scale_x_genomic(
  ...,
  guide = "scalebar",
  unit = "bp",
  sep = " ",
  digits = 3,
  labels = NULL
)

format_bp(
  x,
  unit = "bp",
  sep = " ",
  digits = 3,
  prefixes = c(k = 1000, M = 1e+06, G = 1e+09),
  trim = TRUE,
  scientific = FALSE,
  ...
)

label_bp(unit = "bp", sep = " ", digits = 3)

Arguments

...

Arguments passed on to ggplot2::scale_x_continuous()

guide

A function used to create a guide or its name. See guides() for more information.

unit

unit suffix

sep

separator between number and unit prefix+suffix

digits

a positive integer indicating how many significant digits are to be used for numeric and complex x. The default, NULL, uses getOption("digits"). This is a suggestion: enough decimal places will be used so that the smallest (in magnitude) number has this many significant digits, and also to satisfy nsmall. (For more, notably the interpretation for complex numbers see signif.)

labels

One of the options below. Please note that when labels is a vector, it is highly recommended to also set the breaks argument as a vector to protect against unintended mismatches.

  • 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)

  • An expression vector (must be the same length as breaks). See ?plotmath for details.

  • A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.

x

numeric base-pair value.

prefixes

SI prefixes per thousands.

trim

logical; if FALSE, logical, numeric and complex values are right-justified to a common width: if TRUE the leading blanks for justification are suppressed.

scientific

either a logical specifying whether elements of a real or complex vector should be encoded in scientific format, or an integer penalty (see options("scipen")). Missing values correspond to the current default penalty.

Value

A ggplot2 scale object with bp labels

Character scalar.

A labeller function for genomic data

Functions

  • format_bp(): format a number as human-readable base-pair value.

Examples

library(patchwork)

p0 <- gggenomes(genes = emale_genes) |> pick(1:2) + geom_gene()
#> No seqs provided, inferring seqs from feats
p1 <- p0 + scale_x_genomic("base pairs", guide = "axis", unit = "", sep = "")
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
p2 <- p1 + scale_x_genomic(limits=c(-1000, 5000)) + theme_minimal()
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
p3 <- p0 + scale_x_continuous("regular x-axis")
#> Scale for x is already present.
#> Adding another scale for x, which will replace the existing scale.
p0 + p1 + p2 + p3 + plot_layout(ncol=2)
#> Warning: Removed 40 rows containing missing values or values outside the scale range
#> (`geom_gene()`).

format_bp(c(0, 5e5, 1e6, 1.5e6, 2e6), digits=3, scientific=TRUE)
#> [1] "0.0e+00 Mbp" "5.0e-01 Mbp" "1.0e+00 Mbp" "1.5e+00 Mbp" "2.0e+00 Mbp"