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

Value

a tbl_df with plot coordinates

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() 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 subfeats are in different coordinate

Methods (by class)

as_subfeats(tbl_df): Convert a list of tibbles into a feat layout

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.