geom_coverage {gggenomes}

Draw wiggle ribbons or lines

Description

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

Usage

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. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used the 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.

geom

The geometric object to use to display the data for this layer. When using a ⁠stat_*()⁠ function to construct a layer, the geom argument can be used to override the default coupling between stats and geoms. The geom argument accepts the following:

• A Geom ggproto subclass, for example GeomPoint.

• A string naming the geom. To give the geom as a string, strip the function name of the geom_ prefix. For example, to use geom_point(), give the geom as "point".

• For more information and other ways to specify the geom, see the layer geom 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.

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()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

• Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

• When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

• Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

• The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

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.

Value

A ggplot2 layer with coverage information.

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()

# 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()

# 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()
# Plot varying GC-content along sequences as ribbon
gggenomes(seqs = emale_seqs, feats = emale_gc) +
  geom_wiggle(aes(z = score)) +
  geom_seq()

# 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()

# 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")

# 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")