geom_junction_label_repel: Label junction curves

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

Label junction curves

Description

geom_junction_label_repel() labels junction curves at their midpoint using ggrepel::geom_label_repel(). This can be useful to label and compare junctions (plotted using geom_junction()) with metrics of their usage (e.g. read counts or percent-spliced-in).

Usage

geom_junction_label_repel(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  parse = FALSE,
  ...,
  junction.orientation = "alternating",
  junction.y.max = 1,
  angle = 90,
  ncp = 15,
  box.padding = 0.25,
  label.padding = 0.25,
  point.padding = 1e-06,
  label.r = 0.15,
  label.size = 0.25,
  min.segment.length = 0,
  arrow = NULL,
  force = 1,
  force_pull = 1,
  max.time = 0.5,
  max.iter = 10000,
  max.overlaps = getOption("ggrepel.max.overlaps", default = 10),
  nudge_x = 0,
  nudge_y = 0,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  na.rm = FALSE,
  show.legend = NA,
  direction = c("both", "y", "x"),
  seed = NA,
  verbose = FALSE,
  inherit.aes = TRUE
)

Arguments

mapping	Set of aesthetic mappings created by aes or aes_. If specified and inherit.aes = TRUE (the default), is combined with the default mapping at the top level of the plot. You only need to supply mapping if there isn't a mapping defined for the plot.
data	A data frame. If specified, overrides the default data frame defined at the top level of the plot.
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.
parse	If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath
...	other arguments passed on to layer. There are three types of arguments you can use here: Aesthetics: to set an aesthetic to a fixed value, like colour = "red" or size = 3. Other arguments to the layer, for example you override the default stat associated with the layer. Other arguments passed on to the stat.
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.
box.padding	Amount of padding around bounding box, as unit or number. Defaults to 0.25. (Default unit is lines, but other units can be specified by passing unit(x, "units")).
label.padding	Amount of padding around label, as unit or number. Defaults to 0.25. (Default unit is lines, but other units can be specified by passing unit(x, "units")).
point.padding	Amount of padding around labeled point, as unit or number. Defaults to 0. (Default unit is lines, but other units can be specified by passing unit(x, "units")).
label.r	Radius of rounded corners, as unit or number. Defaults to 0.15. (Default unit is lines, but other units can be specified by passing unit(x, "units")).
label.size	Size of label border, in mm.
min.segment.length	Skip drawing segments shorter than this, as unit or number. Defaults to 0.5. (Default unit is lines, but other units can be specified by passing unit(x, "units")).
arrow	specification for arrow heads, as created by arrow
force	Force of repulsion between overlapping text labels. Defaults to 1.
force_pull	Force of attraction between a text label and its corresponding data point. Defaults to 1.
max.time	Maximum number of seconds to try to resolve overlaps. Defaults to 0.5.
max.iter	Maximum number of iterations to try to resolve overlaps. Defaults to 10000.
max.overlaps	Exclude text labels when they overlap too many other things. For each text label, we count how many other text labels or other data points it overlaps, and exclude the text label if it has too many overlaps. Defaults to 10.
nudge_x, nudge_y	Horizontal and vertical adjustments to nudge the starting position of each text label. The units for nudge_x and nudge_y are the same as for the data units on the x-axis and y-axis.
xlim, ylim	Limits for the x and y axes. Text labels will be constrained to these limits. By default, text labels are constrained to the entire plot area.
na.rm	If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing 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.
direction	"both", "x", or "y" – direction in which to adjust position of labels
seed	Random seed passed to set.seed. Defaults to NA, which means that set.seed will not be called.
verbose	If TRUE, some diagnostics of the repel algorithm are printed
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.

Details

geom_junction_label_repel() requires the following aes(); xstart, xend, y (e.g. transcript name) and label. Under the hood, geom_junction_label_repel() generates the same junction curves as geom_junction() to obtain curve midpoints for labeling. Therefore, it is important that users use the same input data and parameters that alter junction curves (namely junction.orientation, junction.y.max, angle, ncp) for geom_junction_label_repel() that they have used for geom_junction().

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")

# geom_junction_label_repel() can be used to label junctions
base <- sod1_exons %>%
    ggplot(aes(
        xstart = start,
        xend = end,
        y = transcript_name
    )) +
    geom_range() +
    geom_intron(
        data = to_intron(sod1_exons, "transcript_name")
    )

# this can be useful to label junctions with their counts
base +
    geom_junction(
        data = sod1_junctions,
        junction.y.max = 0.5
    ) +
    geom_junction_label_repel(
        data = sod1_junctions,
        aes(label = round(mean_count, 2)),
        junction.y.max = 0.5
    )

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