as_sublinks: Compute a layout for links linking feats

In thackl/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)

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()
everything	set to FALSE to drop optional columns
transform	use if feats and sublinks are in different coordinate spaces, i.e. if matching nucleotide-level annotations to protein level annotations, e.g. genes and protein blast results.

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

thackl/gggenomes documentation built on March 10, 2024, 7:26 a.m.