geom_genemodel: Gene models
In teunbrand/ggnomics: ggnomics

Description Usage Arguments Details Aesthetics See Also Examples

geom_genemodel is a specialised geom for drawing gene models. It draws coding sequences thicker than untranslated regions and styles introns with arrows, lines or chevrons. By default, it separates different overlapping models along the y-axis.

geom_genemodel(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = position_disjoint_ranges(extend = 10000),
  ...,
  intron.style = "arrowline",
  arrow = NULL,
  arrow.freq = unit(4, "mm"),
  chevron.height = 1,
  linejoin = "mitre",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

`mapping`	Set of aesthetic mappings created by `aes()` or `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, as a string.
`position`	Position adjustment, either as a string, or the result of a call to a position adjustment function.
`...`	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.
`intron.style`	By default, introns are displayed as a series of arrows (`"arrowline"`) when a `strand` aesthetic contains `"+"` or `"-"`. Alternatively, a `"chevron"` option is available. In absence of strand information, the intron style defaults to a simple line (`"line"`).
`arrow`	Specification for arrow heads, as created by `arrow`. Only applicable when `intron.style = "arrowline"` (the default). Defaults internally to `grid::arrow(length = grid::unit(2, "mm"))`.
`arrow.freq`	A `unit` object specifying the distance over which arrows should be repeated. Only applicable when `intron.style = "arrowline"`.
`chevron.height`	A `numeric` of length one specifying how high chevrons should rise relative to coding sequences. Only applicable when `intron.style = "chevron"`.
`linejoin`	Line join style (round, mitre, bevel).
`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()`.

The expected input format is that every exon has its own row. The genomic location of the exons are to be given to the xmin aesthetic for start positions and the xmax aesthetic for the end position. Genes are interpreted to be groups of exons specified by the required group aesthetic. Exons that belong to the same group will be connected by introns.

Optionally, a distinction between coding sequences (CDSs) and untranslated regions (UTRs) can be made for each exon by providing the exontype aesthetic. Also, strand information can be used to style introns in the "arrowline" or "chevron" fashion by providing a strand aesthetic, which assumes that "+" should be oriented left-to-right and "-" should be right-to-left. A y aesthetic can be provided to offset the gene models from the x-axis. The thickness aesthetic controls how thick a CDS should be drawn in y-axis units.

Alternatively, this geom can also be used to visualise transcript models, in which case the following recommendations apply. Supply a transcript name or transcript ID to the group aesthetic instead of a gene name or gene ID. Set intron.style = "chevron" which is more appropriate for splice junctions.

geom_genemodel understands the following aesthetics (required aesthetics are in bold, optional aesthetics in italics)

xmax
xmin
group
y
thickness
type
strand
colour
fill
size
linetype
alpha

position_disjoint_ranges

# Using GRanges for exons
require(GenomicRanges)
gm <- example_genemodels()
df <- DataFrame(x = granges(gm), mcols(gm))

ggplot(df) +
    geom_genemodel(aes(x = x, group = name, exontype = type))