gggenomes (version 1.0.1)

geom_seq_break: 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,
  ...
)

Value

A ggplot2 layer with sequence breaks.

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. When using a geom_*() function to construct a layer, the stat argument can be used the override the default coupling between geoms and stats. The stat argument accepts the following:

• A Stat ggproto subclass, for example StatCount.

• A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

• For more information and other ways to specify the stat, see the layer stat documentation.

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()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

• Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

• When constructing a layer using a stat_*() function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

• Inversely, when constructing a layer using a geom_*() function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

• The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

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()