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Draw bin labels

Source: R/geom.R
geom_bin_label.Rd

Put bin labels left of the sequences. nudge_left adds space relative to the total bin width between the label and the seqs, by default 5%. expand_left expands the plot to the left by 20% to make labels visible.

Usage

geom_bin_label(
  mapping = NULL,
  data = bins(),
  hjust = 1,
  size = 3,
  nudge_left = 0.05,
  expand_left = 0.2,
  expand_x = NULL,
  expand_aes = NULL,
  yjust = 0,
  ...
)

Arguments

mapping

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

hjust

Moves the text horizontally

size

of the label

nudge_left

by this much relative to the widest bin

expand_left

by this much relative to the widest bin

expand_x

expand the plot to include this absolute x value

expand_aes

provide custom aes mappings for the expansion (advanced)

yjust

for multiline bins set to 0.5 to center labels on bins, and 1 to align labels to the bottom.

...

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.

Value

Bin labels are added as a text layer/component to the plot.

Details

Set x and expand_x to an absolute position to align all labels at a specific location

Examples

s0 <- read_seqs(list.files(ex("cafeteria"), "Cr.*\\.fa.fai$", full.names = TRUE))
#> Reading 'fai' with `read_fai()`:
#> * file_id: CrBVI.fa [/home/runner/work/_temp/Library/gggenomes/extdata/cafeteria/CrBVI.fa.fai]
#> * file_id: CrCflag.fa [/home/runner/work/_temp/Library/gggenomes/extdata/cafeteria/CrCflag.fa.fai]
#> * file_id: CrE410P.fa [/home/runner/work/_temp/Library/gggenomes/extdata/cafeteria/CrE410P.fa.fai]
#> * file_id: CrRCC970.fa [/home/runner/work/_temp/Library/gggenomes/extdata/cafeteria/CrRCC970.fa.fai]
s1 <- s0 %>% dplyr::filter(length > 5e5)

gggenomes(emale_genes) + geom_seq() + geom_gene() +
  geom_bin_label()
#> No seqs provided, inferring seqs from feats


# make larger labels and extra room on the canvas
gggenomes(emale_genes) + geom_seq() + geom_gene() +
  geom_bin_label(size = 7, expand_left = .4)
#> No seqs provided, inferring seqs from feats


# align labels for wrapped bins:
# top
gggenomes(seqs = s1, infer_bin_id = file_id, wrap = 5e6) +
  geom_seq() + geom_bin_label() + geom_seq_label()


# center
gggenomes(seqs = s1, infer_bin_id = file_id, wrap = 5e6) +
  geom_seq() + geom_bin_label(yjust = .5) + geom_seq_label()


# bottom
gggenomes(seqs = s1, infer_bin_id = file_id, wrap = 5e6) +
  geom_seq() + geom_bin_label(yjust = 1) + geom_seq_label()