geom_link() allows the user to link loci/regions between two sequences/genomes with one another.
Note that by default only links between adjacent sequences are computed and shown.
To compute and show all links between all genomes, set gggenomes(..., adjacent_only=FALSE).
geom_link(
mapping = NULL,
data = links(),
stat = "identity",
position = "identity",
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE,
offset = 0.15,
...
)Arguments
- offset
distance between seq center and link start. Use two values
c(<offset_top>, <offset_bottom>)for different top and bottom offsets
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.
Keep in mind: when start/end is not specified, links will be created between the entire contigs of seq_id and seq_id2
Examples
p <- gggenomes(seqs=emale_seqs, links = emale_ava) + geom_seq()
p + geom_link()
# change offset from seqs
p + geom_link(aes(fill=de, color=de), offset = 0.05) +
scale_fill_viridis_b() + scale_colour_viridis_b()
# combine with flip
p %>% flip(3,4,5) + geom_link()
# compute & show all links among all genomes (not recommended for large dataset)
gggenomes(links=emale_ava, adjacent_only = FALSE) + geom_link()
#> No seqs or feats provided, inferring seqs from links
