Draw wiggle ribbons or lines

Source: R/geom_coverage.R, R/geom_wiggle.R

Visualize data that varies along sequences as ribbons, lines, lineranges, etc.

geom_coverage(
  mapping = NULL,
  data = feats(),
  stat = "coverage",
  geom = "ribbon",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  offset = 0,
  height = 0.2,
  max = base::max,
  ...
)

geom_wiggle(
  mapping = NULL,
  data = feats(),
  stat = "wiggle",
  geom = "ribbon",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  offset = 0,
  height = 0.8,
  bounds = Hmisc::smedian.hilow,
  ...
)

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, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")

geom

The geometric object to use to display the data, either as a ggproto Geom subclass or as a string naming the geom stripped of the geom_ prefix (e.g. "point" rather than "geom_point")

position

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

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.

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. borders().

offset

distance between seq center and wiggle mid/start.

height

distance in plot between lowest and highest point of the wiggle data.

max

geom_coverage uses the function base::max by default, which plots data in positive direction. (base::min Can also be called here when the input data )

...

Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

bounds

geom_wiggle uses mid, low and high boundary values for plotting wiggle data. Can be both a function or a vector returning those three values. Defaults to Hmisc::smedian.hilow.

Details

Geom_wiggle plots the wiggle data in both directions around the median. Geom_coverage plots the data only in positive direction. Both functions use data from the feats' track.

Aesthetics

geom_wiggle() and geom_coverage() understand aesthetics depending on the chosen underlying ggplot geom, by default ggplot2::geom_ribbon(). Other options that play well are for example ggplot2::geom_line(), ggplot2::geom_linerange(), ggplot2::geom_point(). The only required aesthetic is:

  • z

Examples

# Plotting data with geom_coverage with increased height.
gggenomes(seqs = emale_seqs, feats = emale_gc) +
  geom_coverage(aes(z = score), height = 0.5) +
  geom_seq()
#> coverage max
#> • max: 0.88


# In opposite direction by calling base::min and taking the negative values of "score"
gggenomes(seqs = emale_seqs, feats = emale_gc) +
  geom_coverage(aes(z = -score), max = base::min, height = 0.5) +
  geom_seq()
#> coverage max
#> • max: -0.88


# GC-content plotted as points with variable color in geom_coverage
gggenomes(seqs = emale_seqs, feats = emale_gc) +
  geom_coverage(aes(z = score, color = score), height = 0.5, geom = "point") +
  geom_seq()
#> coverage max
#> • max: 0.88

# Plot varying GC-content along sequences as ribbon
gggenomes(seqs=emale_seqs, feats=emale_gc) +
  geom_wiggle(aes(z=score)) +
  geom_seq()
#> wiggle bounds
#> • mid:  0.38
#> • low:  0.2
#> • high: 0.76


# customize color and position
gggenomes(genes=emale_genes, seqs=emale_seqs, feats=emale_gc) +
  geom_wiggle(aes(z=score), fill="lavenderblush3", offset=-.3, height=.5) +
  geom_seq() + geom_gene()
#> wiggle bounds
#> • mid:  0.38
#> • low:  0.2
#> • high: 0.76


# GC-content as line and with variable color
gggenomes(seqs=emale_seqs, feats=emale_gc) +
  geom_wiggle(aes(z=score, color=score), geom="line", bounds=c(.5,0,1)) +
  geom_seq() +
  scale_colour_viridis_b(option="A")
#> wiggle bounds
#> • mid:  0.5
#> • low:  0
#> • high: 1


# or as lineranges
gggenomes(seqs=emale_seqs, feats=emale_gc) +
  geom_wiggle(aes(z=score, color=score), geom="linerange") +
  geom_seq() +
  scale_colour_viridis_b(option="A")
#> wiggle bounds
#> • mid:  0.38
#> • low:  0.2
#> • high: 0.76