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Plot intron lines with strand arrows

Source: R/geom_intron.R
geom_intron.Rd

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(). 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.

...

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.

arrow

specification for arrow heads, as created by grid::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
#>   <fct>       <int>    <int> <fct>  <fct>      <chr>     <chr>          
#> 1 21       42974510 43033931 +      gene       PKNOX1    NA             
#> 2 21       42974510 43033931 +      transcript PKNOX1    PKNOX1-203     
#> 3 21       42974510 42974664 +      exon       PKNOX1    PKNOX1-203     
#> 4 21       43004326 43004432 +      exon       PKNOX1    PKNOX1-203     
#> 5 21       43007491 43007618 +      exon       PKNOX1    PKNOX1-203     
#> 6 21       43013068 43013238 +      exon       PKNOX1    PKNOX1-203     
#> # ℹ 1 more variable: transcript_biotype <chr>

# 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
#>   <fct>       <int>    <int> <fct>  <fct> <chr>     <chr>          
#> 1 21       42974510 42974664 +      exon  PKNOX1    PKNOX1-203     
#> 2 21       43004326 43004432 +      exon  PKNOX1    PKNOX1-203     
#> 3 21       43007491 43007618 +      exon  PKNOX1    PKNOX1-203     
#> 4 21       43013068 43013238 +      exon  PKNOX1    PKNOX1-203     
#> 5 21       43016908 43017007 +      exon  PKNOX1    PKNOX1-203     
#> 6 21       43018133 43018230 +      exon  PKNOX1    PKNOX1-203     
#> # ℹ 1 more variable: transcript_biotype <chr>

# 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_biotype    start
#>   <fct>    <fct>  <chr>  <chr>     <chr>           <chr>                 <int>
#> 1 21       +      intron PKNOX1    PKNOX1-203      protein_coding     42974664
#> 2 21       +      intron PKNOX1    PKNOX1-202      retained_intron    42974664
#> 3 21       +      intron PKNOX1    PKNOX1-201      protein_coding     42974664
#> 4 21       +      intron PKNOX1    PKNOX1-206      retained_intron    42974664
#> 5 21       +      intron PKNOX1    PKNOX1-204      retained_intron    43004432
#> 6 21       +      intron PKNOX1    PKNOX1-203      protein_coding     43004432
#> # ℹ 1 more variable: end <int>

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),
    linewidth = 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
    )