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Draw links between genomes

Source: R/geom_link.R
geom_link.Rd

Draws connections between genomes, such as genome/gene/protein alignments and gene/protein clusters. geom_link() draws links as filled polygons, geom_link_line() draws a single connecting line.

Note that by default only links between adjacent genomes are computed and shown. To compute and show all links between all genomes, set gggenomes(..., adjacent_only=FALSE).

Usage

geom_link(
  mapping = NULL,
  data = links(),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  offset = 0.15,
  ...
)

geom_link_line(
  mapping = NULL,
  data = links(),
  stat = "identity",
  position = "identity",
  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

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.

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 link start. Use two values c(<offset_top>, <offset_bottom>) for different top and bottom offsets

...

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.

Value

A ggplot2 layer with links.

Details

The function calls upon the data stored within the link track. Data frames added to this track have seq_id and seq_id2 as required variables. Optional and recommended variables include start, start2, end, end2, bin_id, bin_id2 and strand.

Note, when start/end is not specified, links will be created between the entire contigs of seq_id and seq_id2.

Examples

p0 <- gggenomes(seqs = emale_seqs, links = emale_ava) + geom_seq()

# default links
p1 <- p0 + geom_link()

# change offset from seqs and color
p2 <- p0 + geom_link(aes(fill = de, color = de), offset = 0.05) +
  scale_fill_viridis_b() + scale_colour_viridis_b()

# combine with flip
p3 <- p0 |> flip(3, 4, 5) +
  geom_link()

# compute & show all links among all genomes
# usually not useful and not recommended for large dataset
p4 <- gggenomes(links = emale_ava, adjacent_only = FALSE) + geom_link()
#> No seqs or feats provided, inferring seqs from links

library(patchwork) # combine plots in one figure
p1 + p2 + p3 + p4 + plot_layout(nrow = 1)

q0 <- gggenomes(emale_genes, emale_seqs) |>
  add_clusters(emale_cogs) +
  geom_seq() + geom_gene()
#> Joining with `by = join_by(feat_id)`

# link gene clusters with polygon
q1 <- q0 + geom_link(aes(fill = cluster_id))

# link gene clusters with lines
q2 <- q0 + geom_link_line(aes(color = cluster_id))

q1 + q2 + plot_layout(nrow = 1, guides = "collect")