as_sublinks: Compute a layout for links linking feats

View source: R/sublinks.R

as_sublinksR Documentation

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 class 'tbl_df'
as_sublinks(
  x,
  seqs,
  feats,
  ...,
  everything = TRUE,
  transform = c("none", "aa2nuc", "nuc2aa"),
  compute_layout = TRUE
)

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

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.

Value

a tbl_df with plot coordinates

Methods (by class)

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


thackl/gggenomes documentation built on Aug. 31, 2024, 9:47 p.m.