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Draw gene models

Source: R/geom_gene.R
geom_gene.Rd

Draw coding sequences, mRNAs and other non-coding features. Supports multi-exon features. CDS and mRNAs in the same group are plotted together. They can therefore also be positioned as a single unit using the position argument.

Usage

geom_gene(
  mapping = NULL,
  data = genes(),
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  size = 2,
  rna_size = size,
  shape = size,
  rna_shape = shape,
  intron_shape = size,
  intron_types = c("CDS", "mRNA", "tRNA", "tmRNA", "ncRNA", "rRNA"),
  cds_aes = NULL,
  rna_aes = NULL,
  intron_aes = NULL,
  ...
)

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. 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(). This method allows for passing extra arguments to the position.

  • A string naming 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.

na.rm

remove na values

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().

size, rna_size

the size of the gene model, aka the height of the polygons. rna_size only applies to non-coding parts of the gene model, defaults to size.

shape, rna_shape

vector of height and width of the arrow tip, defaults to size. If only one value is provided it is recycled. Set '0' to deactivates arrow-shaped tips. rna_shape only applies to non-coding parts of the gene model, defaults to shape.

intron_shape

single value controlling the kink of the intron line. Defaults to size. Set 0 for straight lines between exons.

intron_types

introns will only be computed/drawn for features with types listed here. Set to "CDS" to plot mRNAs as continous features, and set to NA to completely ignore introns.

cds_aes, rna_aes, intron_aes

overwrite aesthetics for different model parts. Need to be wrapped in ggplot2::aes(). NOTE: These remappings are applied after the data has been transformed and mapped by the plot scales (see ggplot2::after_scale()). So you need to map between aesthetic names (not data columns) and with standardized names, i.e. British English spelling. These mappings can be used to dynamically change parts of the gene model. For example, to change the color of introns from a hard-coded "black" to the same color used to fill the CDS you could specify intron_aes=aes(colour = fill). By default, rna_aes is remapped with aes(fill=colorspace::lighten(fill, .5), colour=colorspace::lighten(colour, .5)) to give it a lighter appearence than the corresponding CDS but in the same color.

...

passed to layer params

Value

A ggplot2 layer with genes.

Aesthetics

geom_gene() understands the following aesthetics (required aesthetics are in bold):

Learn more about setting these aesthetics in vignette("ggplot2-specs").

'type' and 'group' (mapped to 'type' and 'geom_id' by default) power the proper recognition of CDS and their corresponding mRNAs so that they can be drawn as one composite object. Overwrite 'group' to plot CDS and mRNAs independently.

'introns' (mapped to 'introns') is used to compute intron/exon boundaries. Use the parameter intron_types if you want to disable introns.

Examples

gggenomes(genes = emale_genes) +
  geom_gene()
#> No seqs provided, inferring seqs from feats


gggenomes(genes = emale_genes) +
  geom_gene(aes(fill = as.numeric(gc_content)), position = "strand") +
  scale_fill_viridis_b()
#> No seqs provided, inferring seqs from feats


g0 <- read_gff3(ex("eden-utr.gff"))
#> Harmonizing attribute names
#> • ID -> feat_id
#> • Name -> name
#> • Parent -> parent_ids
#> • Target -> target
#> Features read
#> # A tibble: 8 × 3
#>   source type                n
#>   <chr>  <chr>           <int>
#> 1 NA     CDS                 5
#> 2 NA     TF_binding_site     1
#> 3 NA     cDNA_match          1
#> 4 NA     exon                5
#> 5 NA     five_prime_UTR      1
#> 6 NA     gene                1
#> 7 NA     mRNA                5
#> 8 NA     three_prime_UTR     1
gggenomes(genes = g0) +
  # all features in the "genes" regardless of type
  geom_feat(data = feats(genes)) +
  annotate("text", label = "geom_feat", x = -15, y = .9) + xlim(-20, NA) +
  # only features in the "genes" of geneish type (implicit `data=genes()`)
  geom_gene() +
  geom_gene_tag(aes(label = ifelse(is.na(type), "<NA>", type)), data = genes(.gene_types = NULL)) +
  annotate("text", label = "geom_gene", x = -15, y = 1) +
  # control which types are returned from the track
  geom_gene(aes(y = 1.1), data = genes(.gene_types = c("CDS", "misc_RNA"))) +
  annotate("text", label = "gene_types", x = -15, y = 1.1) +
  # control which types can have introns
  geom_gene(
    aes(y = 1.2, yend = 1.2),
    data = genes(.gene_types = c("CDS", "misc_RNA")),
    intron_types = "misc_RNA"
  ) +
  annotate("text", label = "intron_types", x = -15, y = 1.2)
#> No seqs provided, inferring seqs from feats
#> Warning: Ignoring unknown aesthetics: yend


# spliced genes
library(patchwork)
gg <- gggenomes(genes = g0)
#> No seqs provided, inferring seqs from feats
gg + geom_gene(position = "pile") +
  gg + geom_gene(aes(fill = type),
    position = "pile",
    shape = 0, intron_shape = 0, color = "white"
  ) +
  # some fine-control on cds/rna/intron after_scale aesthetics
  gg + geom_gene(aes(fill = geom_id),
    position = "pile",
    size = 2, shape = c(4, 3), rna_size = 2, intron_shape = 4, stroke = 0,
    cds_aes = aes(fill = "black"), rna_aes = aes(fill = fill),
    intron_aes = aes(colour = fill, stroke = 2)
  ) +
  scale_fill_viridis_d() +
  # fun with introns
  gg + geom_gene(aes(fill = geom_id), position = "pile", size = 3, shape = c(4, 4)) +
  gg + geom_gene(aes(fill = geom_id),
    position = "pile", size = 3, shape = c(4, 4),
    intron_types = c()
  ) +
  gg + geom_gene(aes(fill = geom_id),
    position = "pile", size = 3, shape = c(4, 4),
    intron_types = "CDS"
  )