as_subfeats: Compute a layout for subfeat data

In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics

Compute a layout for subfeat data

Description

Read subfeat data such as domains or blast hits on genes into a tidy dataframe. Subfeats need to be associated with an already added feat track. The subfeat track itself is internally converted into a new, regular feat track by mapping the start and end coordinates provided relative to their parent feat into coordinates relative to the sequences underlying the parent feats.

Usage

as_subfeats(x, seqs, feats, ..., everything = TRUE)

Arguments

x	subfeat data convertible to a feat layout
seqs	the sequence layout the parent feats map onto.
feats	the parent feats the subfeats map onto.
...	passed on to layout_seqs()
everything	set to FALSE to drop optional columns
transform	use if feats and subfeats are in different coordinate spaces, i.e. if matching nucleotide-level annotations to protein level annotations, e.g. genes and protein blast results.

Details

Obligatory columns are feat_id, start and end. Also recognized are strand and bin_id.

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 and "-" for end < start inputs. 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.