as_sublinks: Compute a layout for links linking feats

In gggenomes: A Grammar of Graphics for Comparative Genomics

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 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

gggenomes documentation built on Sept. 11, 2024, 8:55 p.m.