Add different types of tracks

Usage

add_feats(x, ...)

add_links(x, ..., .adjacent_only = TRUE)

add_subfeats(x, ..., .track_id = "genes", .transform = "aa2nuc")

add_sublinks(x, ..., .track_id = "genes", .transform = "aa2nuc")

add_clusters(x, ..., .track_id = "genes")

Arguments

x: object to add the tracks to (e.g. gggenomes, gggenomes_layout)
...: named data.frames, i.e. genes=gene_df, snps=snp_df
.adjacent_only: indicate whether links should be drawn only between vertically adjacent tracks
.track_id: track_id of the feats that subfeats, sublinks or clusters map to.
.transform: one of "aa2nuc", "none", "nuc2aa"

Value

gggenomes object with added features

Functions

add_feats(): Add feature annotations to sequences
add_links(): Add links connecting sequences, such as whole-genome alignment data.
add_subfeats(): Add features of features, such as gene/protein domains, blast hits to genes/proteins, etc.
add_sublinks(): Add links that connect features, such as protein-protein alignments connecting genes.
add_clusters(): Add gene clusters or other feature groups. Takes a data.frame with at least two required columns cluster_id and feat_id. The data.frame is converted to a link track connecting features belonging to the same cluster over their entire length. Additionally, the data.frame is joined to the parent feature track, adding cluster_id and all additional columns to the parent table.

Examples

# Add some repeat annotations
gggenomes(seqs = emale_seqs) %>%
  add_feats(repeats = emale_tirs) +
  geom_seq() + geom_feat()


# Add all-vs-all whole-genome alignments
gggenomes(seqs = emale_seqs) %>%
  add_links(links = emale_ava) +
  geom_seq() + geom_link()


# Add domains to genes
genes <- tibble::tibble(seq_id = "A", start = 100, end = 200, feat_id = "gene1")
domains <- tibble::tibble(feat_id = "gene1", start = 40, end = 80)
gggenomes(genes = genes) %>% add_subfeats(domains, .transform = "none") +
  geom_gene() + geom_feat()
#> No seqs provided, inferring seqs from feats
#> Only saw `type=NA` in genes and will treat everything as `type="CDS"`.


# Add protein-protein alignments
gggenomes(emale_genes) %>%
  add_sublinks(emale_prot_ava) +
  geom_gene() + geom_link()
#> No seqs provided, inferring seqs from feats
#> Transforming sublinks with "aa2nuc". Disable with `.transform = "none"`


# add clusters
gggenomes(emale_genes, emale_seqs) %>%
  add_clusters(emale_cogs) %>%
  sync() + # works because clusters
  geom_link() + # become links
  geom_seq() +
  # works because cluster info is joined to gene track
  geom_gene(aes(fill = ifelse(is.na(cluster_id), NA,
    stringr::str_glue("{cluster_id} [{cluster_size}]")
  ))) +
  scale_fill_discrete("COGs")
#> Joining with `by = join_by(feat_id)`
#> Flipping: Cflag_017B,BVI_069,BVI_008A