Layout genomes
layout_genomes(
seqs = NULL,
genes = NULL,
feats = NULL,
links = NULL,
infer_bin_id = seq_id,
infer_start = min(start, end),
infer_end = max(start, end),
infer_length = max(start, end),
adjacent_only = TRUE,
...
)gggenomes_layout object
A data.frame or a character vector with paths to files containing sequence data. Data columns:
required: seq_id,length
recognized: bin_id,start,end,strand
A data.frame, a list of data.frames, or a character vector with paths to files containing gene data. Each item is added as feature track.
For a single data.frame the track_id will be "genes" and "feats", respectively. For a list, track_ids are parsed from the list names, or if names are missing from the name of the variable containing each data.frame. Data columns:
required: seq_id,start,end
recognized: strand,bin_id,feat_id,introns
A data.frame or a character vector with paths to files containing link data. Each item is added as links track. Data columns:
required: seq_id,seq_id2
recognized: start,end,bin_id,start2,end2,bin_id2,strand
used to infer pseudo seqs if only feats or links are provided, or if no bin_id column was provided. The expressions are evaluated in the context of the first feat or link track.
By default subregions of sequences from the first to the last feat/link
are generated. Set infer_start to 0 to show all sequences from their
true beginning.
Indicates whether links should be created between adjacent sequences/chromosomes only.
By default it is set to adjacent_only = TRUE. If FALSE, links will be created between all sequences
(not recommended for large data sets)
additional parameters, passed to layout