geom_link: Draw links between genomes

In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics

Draw links between genomes

Description

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

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()

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()

# 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")

thackl/gggenomes documentation built on March 10, 2024, 7:26 a.m.