geom_gene_label: Draw feat/link labels
In gggenomes: A Grammar of Graphics for Comparative Genomics

geom_gene_label

R Documentation

Draw feat/link labels

Description

These geom_..._label() functions able the user to plot labels/text at individual features and/or links. Users have to indicate how to label the features/links by specifying label = ... or ⁠aes(label = ...⁠

Position of labels can be adjusted with arguments such as vjust, hjust, angle, nudge_y, etc. Also check out geom_bin_label(), geom_seq_label() or geom_feat_text() given their resemblance.

Usage

geom_gene_label(
  mapping = NULL,
  data = genes(),
  angle = 45,
  hjust = 0,
  nudge_y = 0.1,
  size = 6,
  ...
)

geom_feat_label(
  mapping = NULL,
  data = feats(),
  angle = 45,
  hjust = 0,
  nudge_y = 0.1,
  size = 6,
  ...
)

geom_link_label(
  mapping = NULL,
  data = links(),
  angle = 0,
  hjust = 0.5,
  vjust = 0.5,
  size = 4,
  repel = FALSE,
  ...
)

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)`).
`angle`	Defines the angle in which the text will be placed. *Note
`hjust`	Moves the text horizontally
`nudge_y`	Moves the text vertically an entire contig/sequence. (e.g. `nudge_y = 1` places the text to the contig above)
`size`	of the label
`...`	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.
`vjust`	Moves the text vertically
`repel`	use ggrepel to avoid overlaps