Read AliTV .json file — read

this file contains sequences, links and (optionally) genes

Usage

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()
#> Only saw `type=NA` in genes and will treat everything as `type="CDS"`.

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)
#> Only saw `type=NA` in genes and will treat everything as `type="CDS"`.