geom_feat {gggenomes}

Draw feats

Description

geom_feat() allows the user to draw (additional) features to the plot/graph. For example, specific regions within a sequence (e.g. transposons, introns, mutation hotspots) can be highlighted by color, size, etc..

Usage

geom_feat(
  mapping = NULL,
  data = feats(),
  stat = "identity",
  position = "pile",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

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

feat_layout: Uses first data frame stored in the feats track by default.

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.

position

describes how the position of different plotted features are adjusted. By default it uses "pile", but different ggplot2 position adjustments, such as ⁠"identity⁠ or "jitter" can be used as well.

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().

...

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.

Details

geom_feat uses ggplot2::geom_segment under the hood. As a result, different aesthetics such as alpha, linewidth, color, etc. can be called upon to modify the visualization of the data.

By default, the function uses the first feature track.

Value

A ggplot2 layer with features.

Examples

# Plotting data from the feats' track with adjusted linewidth and color
gggenomes(seqs = emale_seqs, feats = emale_ngaros) +
  geom_seq() +
  geom_feat(linewidth = 5, color = "darkred")

# Geom_feat can be called several times as well, when specified what data should be used
gggenomes(seqs = emale_seqs, feats = list(emale_ngaros, emale_tirs)) +
  geom_seq() +
  geom_feat(linewidth = 5, color = "darkred") + # uses first feature track
  geom_feat(data = feats(emale_tirs))

# Additional notes to feats can be added with functions such as: geom_feat_note / geom_feat_text
gggenomes(seqs = emale_seqs, feats = list(emale_ngaros, emale_tirs)) +
  geom_seq() +
  geom_feat(color = "darkred") +
  geom_feat(data = feats(emale_tirs), color = "darkblue") +
  geom_feat_note(data = feats(emale_ngaros), label = "repeat region", size = 4)

# Different position adjustments with a simple dataset
exampledata <- tibble::tibble(
  seq_id = c(rep("A", 3), rep("B", 3), rep("C", 3)),
  start = c(0, 30, 15, 40, 80, 20, 30, 50, 70),
  end = c(30, 90, 60, 60, 100, 80, 60, 90, 120)
)

gggenomes(feats = exampledata) +
  geom_feat(position = "identity", alpha = 0.5, linewidth = 0.5) +
  geom_bin_label()