coord_polar

[thackl]

Originally posted by @iferres in https://github.com/thackl/gggenomes/issues/85#issuecomment-938697228

I assume the following feature request is not trivial at all, but have you considered ... + coord_polar() to draw circularized contigs? Playing with the package (and diving into the source code) I found that the following kinda works:

library(gggenomes) 

s0 <- tibble(
  gene_id = letters[1:6],
  bin_id = c("A", "A", "B", "B", "B", "B"),
  seq_id = factor(c("A1", "A1", "B1", "B1", "B2", "B2"), levels = c("A1", "B2", "B1")), # set factor to order contigs
  feat_id = c("a1","a2","b3", "b4", "b1", "b2"),
  start = c(1, 20, 1, 50, 1, 20),
  end = c(10, 30, 40, 70, 10, 30),
  strand = c(1, 1, 1, 1, 1, 1),
  length = c(1000, 1000, 1000, 1000, 1000, 1000)
)

gggenomes(s0) + 
  geom_seq() + 
  gggenomes:::geom_gene2() + 
  coord_polar() # + 
  # facet_wrap(~bin_id)

but I guess is experimental and there's a lot to work with to make it stable and user friendly, isn't it?

[thackl]

Yes, I thought about it and, yep, your last sentence perfectly sums it up :D.

Here's something I put together playing around before. There's definitely potential, but also a lot of things that break (like geom_gene()). At this point it's not high enough up on my priority list to put in the effort and fully implement it. But it might already be useful to some users to provide guidance on how to explore it as an experimental feature (as you did)

gggenomes(emale_genes %>% mutate(gene_id=feat_id), emale_seqs[1:5,], feats=emale_gc) %>%
  add_clusters(emale_cogs) %>%
  flip_by_links() +
  geom_seq() +
  geom_wiggle(aes(z=score, color=score), geom="linerange", offset=-.4) +
  geom_link(offset=c(0.2,0.2), color=NA) +
  gggenomes:::geom_gene2() +
  coord_polar() + ylim(-2, NA) + xlim(-9000,NA) +
  geom_bin_label(aes(x=0, label=paste0(bin_id, "   ")), angle=-90, hjust=1, vjust=.5, nudge_left = 0.02) +
  scale_colour_viridis_b(option="A")