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$links) +
geom_seq() +
geom_bin_label() +
geom_gene(aes(fill=class)) +
geom_link()
#> Only saw `type=NA` in genes and will treat everything as `type="CDS"`.
p <- gggenomes(ali$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"`.
