as_sublinks | R Documentation |
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.
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
)
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 |
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 |
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.
a tbl_df with plot coordinates
as_sublinks(tbl_df)
: Convert a list of tibbles into a link layout
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