R: Add text to genes, features, etc.

geom_feat_text {gggenomes}

R Documentation

Add text to genes, features, etc.

Description

The functions below are useful for labeling features/genes in plots. Users have to call on aes(label = ...) or (label = ...) to define label's text Based on the function, the label will be placed at a specific location:

geom_..._text() will plot text in the middle of the feature.
geom_..._tag() will plot text on top of the feature, with a 45 degree angle.
geom_..._note() will plot text under the feature at the left side.

The ... can be either replaced with feat or gene depending on which track the user wants to label.

With arguments such as hjust, vjust, angle, and nudge_y, the user can also manually change the position of the text.

Usage

geom_feat_text(
  mapping = NULL,
  data = feats(),
  stat = "identity",
  position = "identity",
  ...,
  parse = FALSE,
  check_overlap = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_feat_tag(
  mapping = NULL,
  data = feats(),
  stat = "identity",
  position = "identity",
  hjust = 0,
  vjust = 0,
  angle = 45,
  nudge_y = 0.03,
  xjust = 0.5,
  strandwise = TRUE,
  ...,
  parse = FALSE,
  check_overlap = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_feat_note(
  mapping = NULL,
  data = feats(),
  stat = "identity",
  position = "identity",
  hjust = 0,
  vjust = 1,
  nudge_y = -0.03,
  xjust = 0,
  strandwise = FALSE,
  ...,
  parse = FALSE,
  check_overlap = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_gene_text(
  mapping = NULL,
  data = genes(),
  stat = "identity",
  position = "identity",
  ...,
  parse = FALSE,
  check_overlap = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_gene_tag(
  mapping = NULL,
  data = genes(),
  stat = "identity",
  position = "identity",
  hjust = 0,
  vjust = 0,
  angle = 45,
  nudge_y = 0.03,
  xjust = 0.5,
  strandwise = TRUE,
  ...,
  parse = FALSE,
  check_overlap = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_gene_note(
  mapping = NULL,
  data = genes(),
  stat = "identity",
  position = "identity",
  hjust = 0,
  vjust = 1,
  nudge_y = -0.03,
  xjust = 0,
  strandwise = FALSE,
  ...,
  parse = FALSE,
  check_overlap = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

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)`).
`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.
`position`	A position adjustment to use on the data for this layer. Cannot be jointy specified with `nudge_x` or `nudge_y`. This can be used in various ways, including to prevent overplotting and improving the display. The `position` argument accepts the following: The result of calling a position function, such as `position_jitter()`. A string nameing the position adjustment. To give the position as a string, strip the function name of the `position_` prefix. For example, to use `position_jitter()`, give the position as `"jitter"`. For more information and other ways to specify the position, see the layer position documentation.
`...`	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.
`parse`	If `TRUE`, the labels will be parsed into expressions and displayed as described in `?plotmath`.
`check_overlap`	If `TRUE`, text that overlaps previous text in the same layer will not be plotted. `check_overlap` happens at draw time and in the order of the data. Therefore data should be arranged by the label column before calling `geom_text()`. Note that this argument is not supported by `geom_label()`.
`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()`.
`hjust`	Moves the text horizontally
`vjust`	Moves the text vertically
`angle`	Defines the angle in which the text will be placed. *Note
`nudge_y`	Moves the text vertically an entire contig/sequence. (e.g. `nudge_y = 1` places the text to the contig above)
`xjust`	Move text in x direction
`strandwise`	plotting of feature tags

Details

These labeling functions use ggplot2::geom_text() under the hood. Any changes to the aesthetics of the text can be performed in a ggplot2 manner.

Value

A ggplot2 layer with gene text.

A ggplot2 layer with feature tags.

A ggplot2 layer with feature notes.

A ggplot2 layer with gene text.

A ggplot2 layer with gene tags.

A ggplot2 layer with gene notes.

Examples

# example data
genes <- tibble::tibble(
  seq_id = c("A", "A", "A", "B", "B", "C"),
  start = c(20, 40, 80, 30, 10, 60),
  end = c(30, 70, 85, 40, 15, 90),
  feat_id = c("A1", "A2", "A3", "B1", "B2", "C1"),
  type = c("CDS", "CDS", "CDS", "CDS", "CDS", "CDS"),
  name = c("geneA", "geneB", "geneC", "geneA", "geneC", "geneB")
)

seqs <- tibble::tibble(
  seq_id = c("A", "B", "C"),
  start = c(0, 0, 0),
  end = c(100, 100, 100),
  length = c(100, 100, 100)
)

# basic plot creation
plot <- gggenomes(seqs = seqs, genes = genes) +
  geom_bin_label() +
  geom_gene()

# geom_..._text
plot + geom_gene_text(aes(label = name))

# geom_..._tag
plot + geom_gene_tag(aes(label = name))

# geom_..._note
plot + geom_gene_note(aes(label = name))

# with horizontal adjustment (`hjust`), vertical adjustment (`vjust`)
plot + geom_gene_text(aes(label = name), vjust = -2, hjust = 1)

# using `nudge_y` and and `angle` adjustment
plot + geom_gene_text(aes(label = name), nudge_y = 1, angle = 10)

# labeling with manual input
plot + geom_gene_text(label = c("This", "is", "an", "example", "test", "test"))

[Package gggenomes version 1.0.0 Index]