geom_seq_label {gggenomes}

Draw seq labels

Description

This function will put labels at each individual sequence. By default it will plot the seq_id as label, but users are able to change this manually.

Position of the label/text can be adjusted with the different arguments (e.g. vjust, hjust, angle, etc.)

Usage

geom_seq_label(
  mapping = NULL,
  data = seqs(),
  hjust = 0,
  vjust = 1,
  nudge_y = -0.15,
  size = 2.5,
  ...
)

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)).

hjust

Moves the text horizontally

vjust

Moves the text vertically

nudge_y

Moves the text vertically an entire contig/sequence. (e.g. nudge_y = 1 places the text to the contig above)

size

of the label

...

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

This labeling function uses ggplot2::geom_text() under the hood. Any changes to the aesthetics of the text can be performed in a ggplot2 manner.

Value

Sequence labels are added as a text layer/component to the plot.

Examples

# example data
seqs <- tibble::tibble(
  bin_id = c("A", "A", "A", "B", "B", "B", "B", "C", "C"),
  seq_id = c("A1", "A2", "A3", "B1", "B2", "B3", "B4", "C1", "C2"),
  start = c(0, 100, 200, 0, 50, 150, 250, 0, 400),
  end = c(100, 200, 400, 50, 100, 250, 300, 300, 500),
  length = c(100, 100, 200, 50, 50, 100, 50, 300, 100)
)

# example plot using geom_seq_label
gggenomes(seqs = seqs) +
  geom_seq() +
  geom_seq_label()

# changing default label to `length` column
gggenomes(seqs = seqs) +
  geom_seq() +
  geom_seq_label(aes(label = length))

# with horizontal adjustment
gggenomes(seqs = seqs) +
  geom_seq() +
  geom_seq_label(hjust = -5)

# with wrapping at 300
gggenomes(seqs = seqs, wrap = 300) +
  geom_seq() +
  geom_seq_label()