Plot intron lines with strand arrows

geom_intron() draws horizontal lines with central arrows that are designed to represent introns. In combination with geom_range()/geom_half_range(), these geoms form the core components for visualizing transcript structures.

Usage

geom_intron(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  arrow = grid::arrow(ends = "last", length = grid::unit(0.1, "inches")),
  arrow.fill = NULL,
  lineend = "butt",
  linejoin = "round",
  na.rm = FALSE,
  arrow.min.intron.length = 0,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

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.

arrow

specification for arrow heads, as created by arrow().

arrow.fill

fill colour to use for the arrow head (if closed). NULL means use colour aesthetic.

lineend

Line end style (round, butt, square).

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.

arrow.min.intron.length

integer() the minimum required width of an intron for a strand arrow to be drawn. This can be useful to remove strand arrows on short introns that overlap adjacent exons.

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().

Value

the return value of a geom_* function is not intended to be directly handled by users. Therefore, geom_* functions should never be executed in isolation, rather used in combination with a ggplot2::ggplot() call.

Details

geom_intron() requires the following aes(); xstart, xend and y (e.g. transcript name). If users do not have intron co-ordinates, these can be generated from the corresponding exons using to_intron(). The strand option (one of "+" or "-") adjusts the arrow direction to match the direction of transcription. The arrow.min.intron.length parameter can be useful to remove strand arrows that overlap exons, which can be a problem if plotted introns include those that are relatively short.

Examples

library(magrittr)
library(ggplot2)

# to illustrate the package's functionality
# ggtranscript includes example transcript annotation
pknox1_annotation %>% head()
#> # A tibble: 6 × 8
#>   seqnames  start    end strand type  gene_name transcript_name transcript_biot…
#>   <fct>     <int>  <int> <fct>  <fct> <chr>     <chr>           <chr>           
#> 1 21       4.30e7 4.30e7 +      gene  PKNOX1    NA              NA              
#> 2 21       4.30e7 4.30e7 +      tran… PKNOX1    PKNOX1-203      protein_coding  
#> 3 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  
#> 4 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  
#> 5 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  
#> 6 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  

# extract exons
pknox1_exons <- pknox1_annotation %>% dplyr::filter(type == "exon")
pknox1_exons %>% head()
#> # A tibble: 6 × 8
#>   seqnames  start    end strand type  gene_name transcript_name transcript_biot…
#>   <fct>     <int>  <int> <fct>  <fct> <chr>     <chr>           <chr>           
#> 1 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  
#> 2 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  
#> 3 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  
#> 4 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  
#> 5 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  
#> 6 21       4.30e7 4.30e7 +      exon  PKNOX1    PKNOX1-203      protein_coding  

# to_intron() is a helper function included in ggtranscript
# which is useful for converting exon co-ordinates to introns
pknox1_introns <- pknox1_exons %>% to_intron(group_var = "transcript_name")
pknox1_introns %>% head()
#> # A tibble: 6 × 8
#>   seqnames strand type  gene_name transcript_name transcript_biot…  start    end
#>   <fct>    <fct>  <chr> <chr>     <chr>           <chr>             <int>  <int>
#> 1 21       +      intr… PKNOX1    PKNOX1-203      protein_coding   4.30e7 4.30e7
#> 2 21       +      intr… PKNOX1    PKNOX1-202      retained_intron  4.30e7 4.30e7
#> 3 21       +      intr… PKNOX1    PKNOX1-201      protein_coding   4.30e7 4.30e7
#> 4 21       +      intr… PKNOX1    PKNOX1-206      retained_intron  4.30e7 4.30e7
#> 5 21       +      intr… PKNOX1    PKNOX1-204      retained_intron  4.30e7 4.30e7
#> 6 21       +      intr… PKNOX1    PKNOX1-203      protein_coding   4.30e7 4.30e7

base <- pknox1_introns %>%
    ggplot(aes(
        xstart = start,
        xend = end,
        y = transcript_name
    ))

# by default, geom_intron() assumes introns originate from the "+" strand
base + geom_intron()


# however this can be modified using the strand option
base + geom_intron(strand = "-")


# strand can also be set as an aes()
base + geom_intron(aes(strand = strand))


# as a ggplot2 extension, ggtranscript geoms inherit the
# the functionality from the parameters and aesthetics in ggplot2
base + geom_intron(
    aes(colour = transcript_name),
    size = 1
)


# together, geom_range() and geom_intron() are designed to visualize
# the core components of transcript annotation
pknox1_exons %>%
    ggplot(aes(
        xstart = start,
        xend = end,
        y = transcript_name
    )) +
    geom_range() +
    geom_intron(
        data = pknox1_introns
    )


# for short introns, sometimes strand arrows will overlap exons
# to avoid this, users can set the arrow.min.intron.length parameter
pknox1_exons %>%
    ggplot(aes(
        xstart = start,
        xend = end,
        y = transcript_name
    )) +
    geom_range() +
    geom_intron(
        data = pknox1_introns,
        arrow.min.intron.length = 3500
    )