as_sublinks: Compute a layout for links linking feats

Description

Reads sublinks connecting feats such as all-vs-all protein blasts into a tidy dataframe. sublinks need to be associated with an already added feat track. The sublinks are internally converted into a regular link track by mapping the feat-based start and end coordinates to coordinates relative to the sequences underlying the linked feats.

Usage

as_sublinks(x, seqs, feats, ..., everything = TRUE)
# S3 method for tbl_df
as_sublinks(
  x,
  seqs,
  feats,
  ...,
  everything = TRUE,
  transform = c("none", "aa2nuc", "nuc2aa"),
  compute_layout = TRUE
)

Value

a tbl_df with plot coordinates

Arguments

x: sublink data convertible to a link layout
seqs: the sequence layout the linked feats map onto.
feats: the feats the sublinks map onto.
...: passed on to layout_seqs() spaces, i.e. if matching nucleotide-level annotations to protein level annotations, e.g. genes and protein blast results.
everything: set to FALSE to drop optional columns
transform: use if feats and sublinks are in different coordinate
compute_layout: set to FALSE to skip layout computation

Methods (by class)

as_sublinks(tbl_df): Convert a list of tibbles into a link layout

Details

The only obligatory columns are feat_id & feat_id2. Also recognized are start/end, start2/end2 and strand.

Note start and end for every record will be coerced so that start < end. If no strand was provided, strand will be added and set to "+" for records that initially had start < end == start2 < end2 and "-" otherwise. If strand was provided, start and end will be reorganized to conform with start < end without any additional effect.