geom_seq_break: Decorate truncated sequences

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

Decorate truncated sequences

Description

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.

Usage

geom_seq_break(
  mapping_start = NULL,
  mapping_end = NULL,
  data_start = seqs(start > 1),
  data_end = seqs(end < length),
  label = "/",
  size = 4,
  hjust = 0.75,
  family = "sans",
  stat = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

Arguments

mapping_start	optional start mapping
mapping_end	optional end mapping
data_start	seq_layout of sequences for which to decorate the start. default: seqs(start >1)
data_end	seq_layout of sequences for which to decorate the end. default: seqs(end < length)
label	the character to decorate ends with. Provide two values for different start and end decorations, e.g. label=c("]", "[").
size	of the text
hjust	Moves the text horizontally
family	font family of the text
stat	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")
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
show.legend	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.
inherit.aes	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.

Examples

# decorate breaks created with focus()
gggenomes(emale_genes, emale_seqs) |>
  focus(.expand=1e3, .max_dist = 1e3) +
  geom_seq() + geom_gene() +
  geom_seq_break()

# 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")

# 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()

thackl/gggenomes documentation built on March 10, 2024, 7:26 a.m.