gggenomes
gggenomes copied to clipboard
flip_by_links() is not working
Hi
I have observed a different behavior regarding flip_by_links() than before. I'm sorry if it's my mistake.
library(gggenomes)
# to inspect the example data shipped with gggenomes
data(package="gggenomes")
gggenomes(emale_genes, emale_seqs, emale_tirs, emale_ava) %>%
add_feats(ngaros=emale_ngaros, gc=emale_gc) %>%
add_sublinks(emale_prot_ava) %>%
flip_by_links() +
geom_feat(position="identity", size=6) +
geom_seq() +
geom_link(data=links(2)) +
geom_bin_label() +
geom_gene(aes(fill=name)) +
geom_gene_tag(aes(label=name), nudge_y=0.1, check_overlap = TRUE) +
geom_feat(data=feats(ngaros), alpha=.3, size=10, position="identity") +
geom_feat_note(aes(label="Ngaro-transposon"), feats(ngaros),
nudge_y=.1, vjust=0) +
geom_ribbon(aes(x=(x+xend)/2, ymax=y+.24, ymin=y+.38-(.4*score),
group=seq_id, linetype="GC-content"), feats(gc),
fill="lavenderblush4", position=position_nudge(y=-.1)) +
scale_fill_brewer("Genes", palette="Dark2", na.value="cornsilk3")
Also, it seems that flip_by_links() is not working in the official references.
I appreciate any help you can provide.
Keigo
I can confirm that this is a bug. It seems to be related to providing both seqs and genes at the same time. Otherwise flip_by_links seems to work fine. Unfortunately, I haven't gotten to the bottom of the problem yet...