geom_seq_break()
adds decorations to the ends of truncated sequences. These
could arise from zooming onto sequence loci with focus()
, or manually
annotating sequences with start > 1 and/or end < length.
optional start mapping
optional end mapping
seq_layout of sequences for which to decorate the start.
default: seqs(start >1)
seq_layout of sequences for which to decorate the end.
default: seqs(end < length)
the character to decorate ends with. Provide two values for
different start and end decorations, e.g. label=c("]", "[")
.
of the text
Moves the text horizontally
font family of the text
The statistical transformation to use on the data for this
layer, either as a ggproto
Geom
subclass or as a string naming the
stat stripped of the stat_
prefix (e.g. "count"
rather than
"stat_count"
)
If FALSE
, the default, missing values are removed with
a warning. If TRUE
, missing values are silently removed.
logical. Should this layer be included in the legends?
NA
, the default, includes if any aesthetics are mapped.
FALSE
never includes, and TRUE
always includes.
It can also be a named logical vector to finely select the aesthetics to
display.
If FALSE
, overrides the default aesthetics,
rather than combining with them. This is most useful for helper functions
that define both data and aesthetics and shouldn't inherit behaviour from
the default plot specification, e.g. borders()
.
Other arguments passed on to layer()
. These are
often aesthetics, used to set an aesthetic to a fixed value, like
colour = "red"
or size = 3
. They may also be parameters
to the paired geom/stat.
# decorate breaks created with focus()
gggenomes(emale_genes, emale_seqs) |>
focus(.expand=1e3, .max_dist = 1e3) +
geom_seq() + geom_gene() +
geom_seq_break()
#> Showing 10 loci with the following size distribution
#> • min: 3853
#> • q25: 9284
#> • med: 12695
#> • q75: 18007
#> • max: 21311
# customize decorations
gggenomes(emale_genes, emale_seqs) |>
focus(.expand=1e3, .max_dist = 1e3) +
geom_seq() + geom_gene() +
geom_seq_break(label=c("[", "]"), size=3, color="#1b9e77")
#> Showing 10 loci with the following size distribution
#> • min: 3853
#> • q25: 9284
#> • med: 12695
#> • q75: 18007
#> • max: 21311
# decorate manually truncated sequences
s0 <- tibble::tribble(
# start/end define regions, i.e. truncated contigs
~bin_id, ~seq_id, ~length, ~start, ~end,
"complete_genome", "chromosome_1_long_trunc_2side", 1e5, 1e4, 2.1e4,
"fragmented_assembly", "contig_1_trunc_1side", 1.3e4, .9e4, 1.3e4,
"fragmented_assembly", "contig_2_short_complete", 0.3e4, 1, 0.3e4,
"fragmented_assembly", "contig_3_trunc_2sides", 2e4, 1e4, 1.4e4
)
l0 <- tibble::tribble(
~seq_id, ~start, ~end, ~seq_id2, ~start2, ~end2,
"chromosome_1_long_trunc_2side", 1.1e4, 1.4e4,
"contig_1_trunc_1side", 1e4, 1.3e4,
"chromosome_1_long_trunc_2side", 1.4e4, 1.7e4,
"contig_2_short_complete", 1, 0.3e4,
"chromosome_1_long_trunc_2side", 1.7e4, 2e4,
"contig_3_trunc_2sides", 1e4, 1.3e4
)
gggenomes(seqs=s0, links=l0) +
geom_seq() + geom_link() +
geom_seq_label(nudge_y=-.05) +
geom_seq_break()