geom_junction: Plot junction curves

In dzhang32/ggtranscript: Visualizing Transcript Structure and Annotation using 'ggplot2'

Plot junction curves

Description

geom_junction() draws curves that are designed to represent junction reads from RNA-sequencing data. It can be useful to overlay junction data on transcript annotation (plotted using geom_range()/geom_half_range() and geom_intron()) to understand which splicing events or transcripts have support from RNA-sequencing data.

Usage

geom_junction(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  junction.orientation = "alternating",
  junction.y.max = 1,
  angle = 90,
  ncp = 15,
  na.rm = FALSE,
  orientation = NA,
  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.
junction.orientation	character() one of "alternating", "top" or "bottom", specifying where the junctions will be plotted with respect to each transcript (y).
junction.y.max	double() the max y-value of each junction curve. It can be useful to adjust this parameter when junction curves overlap with one another/other transcripts or extend beyond the plot margins.
angle	A numeric value between 0 and 180, giving an amount to skew the control points of the curve. Values less than 90 skew the curve towards the start point and values greater than 90 skew the curve towards the end point.
ncp	The number of control points used to draw the curve. More control points creates a smoother curve.
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
orientation	The orientation of the layer. The default (NA) automatically determines the orientation from the aesthetic mapping. In the rare event that this fails it can be given explicitly by setting orientation to either "x" or "y". See the Orientation section for more detail.
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().
...	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.

Details

geom_junction() requires the following aes(); xstart, xend and y (e.g. transcript name). geom_junction() curves can be modified using junction.y.max, which can be useful when junctions overlap one another/other transcripts or extend beyond the plot margins. By default, junction curves will alternate between being plotted on the top and bottom of each transcript (y), however this can be modified via junction.orientation.

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.

Examples

library(magrittr)
library(ggplot2)

# to illustrate the package's functionality
# ggtranscript includes example transcript annotation
sod1_annotation %>% head()

# as well as a set of example (unannotated) junctions
# originating from GTEx and downloaded via the Bioconductor package snapcount
sod1_junctions

# extract exons
sod1_exons <- sod1_annotation %>% dplyr::filter(
    type == "exon",
    transcript_name == "SOD1-201"
)
sod1_exons %>% head()

# add transcript_name to junctions for plotting
sod1_junctions <- sod1_junctions %>%
    dplyr::mutate(transcript_name = "SOD1-201")

# junctions can be plotted as curves using geom_junction()
base <- sod1_junctions %>%
    ggplot2::ggplot(ggplot2::aes(
        xstart = start,
        xend = end,
        y = transcript_name
    ))

# sometimes, depending on the number and widths of transcripts and junctions
# junctions will go overlap one another or extend beyond the plot margin
base + geom_junction()

# in such cases, junction.y.max can be adjusted to modify the max y of curves
base + geom_junction(junction.y.max = 0.5)

# ncp can be used improve the smoothness of curves
base + geom_junction(junction.y.max = 0.5, ncp = 30)

# junction.orientation controls where the junction are plotted
# with respect to each transcript
# either alternating (default), or on the top or bottom
base + geom_junction(junction.orientation = "top", junction.y.max = 0.5)
base + geom_junction(junction.orientation = "bottom", junction.y.max = 0.5)

# it can be useful useful to overlay junction curves onto existing annotation
# plotted using geom_range() and geom_intron()
base <- sod1_exons %>%
    ggplot(aes(
        xstart = start,
        xend = end,
        y = transcript_name
    )) +
    geom_range() +
    geom_intron(
        data = to_intron(sod1_exons, "transcript_name")
    )

base + geom_junction(
    data = sod1_junctions,
    junction.y.max = 0.5
)

# as a ggplot2 extension, ggtranscript geoms inherit the
# the functionality from the parameters and aesthetics in ggplot2
# this can be useful when mapping junction thickness to their counts
base + geom_junction(
    data = sod1_junctions,
    aes(linewidth = mean_count),
    junction.y.max = 0.5,
    colour = "purple"
) +
    scale_linewidth(range = c(0.1, 1))

# it can be useful to combine geom_junction() with geom_half_range()
sod1_exons %>%
    ggplot(aes(
        xstart = start,
        xend = end,
        y = transcript_name
    )) +
    geom_half_range() +
    geom_intron(
        data = to_intron(sod1_exons, "transcript_name")
    ) +
    geom_junction(
        data = sod1_junctions,
        aes(linewidth = mean_count),
        junction.y.max = 0.5,
        junction.orientation = "top",
        colour = "purple"
    ) +
    scale_linewidth(range = c(0.1, 1))

dzhang32/ggtranscript documentation built on Aug. 29, 2024, 2:43 a.m.