this file contains sequences, links and (optionally) genes

read_alitv(file)

Arguments

file

path to json

Value

list with seqs, genes, and links

Examples

ali <- read_alitv("https://alitvteam.github.io/AliTV/d3/data/chloroplasts.json")
gggenomes(ali$genes, ali$seqs, links=ali$links) +
  geom_seq() +
  geom_bin_label() +
  geom_gene(aes(fill=class)) +
  geom_link()

p <- gggenomes(ali$genes, ali$seqs, links=ali$links) +
  geom_seq() +
  geom_bin_label() +
  geom_gene(aes(color=class)) +
  geom_link(aes(fill=identity)) +
  scale_fill_distiller(palette="RdYlGn", direction = 1)
p %>% flip_seqs(5) %>% pick_seqs(1,3,2,4,5,6,7,8)