geom_diagonal_wide_arc: Draw an area defined by an upper and lower diagonal into an...

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

Draw an area defined by an upper and lower diagonal into an arc

Description

The geom_diagonal_wide_arc() function draws a thick diagonal, that is, a polygon confined between a lower and upper diagonal. As with the diagonal functions in ggforce, the wide diagonal variant is horizontal. This function joins two adjacent diagonals into one wider arc.

Usage

stat_diagonal_wide_arc(
  mapping = NULL,
  data = NULL,
  geom = "shape",
  position = "identity",
  n = 100,
  strength = 0.5,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

geom_diagonal_wide_arc(
  mapping = NULL,
  data = NULL,
  stat = "diagonal_wide_arc",
  position = "identity",
  n = 100,
  na.rm = FALSE,
  strength = 0.5,
  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)).
geom	The geometric object to use to display the data for this layer. When using a ⁠stat_*()⁠ function to construct a layer, the geom argument can be used to override the default coupling between stats and geoms. The geom argument accepts the following: A Geom ggproto subclass, for example GeomPoint. A string naming the geom. To give the geom as a string, strip the function name of the geom_ prefix. For example, to use geom_point(), give the geom as "point". For more information and other ways to specify the geom, see the layer geom documentation.
position	Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
n	The number of points to create for each of the bounding diagonals
strength	The proportion to move the control point along the x-axis towards the other end of the bezier curve
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
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(). 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.
stat	The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")

Aesthetics

geom_diagonal_wide_arc understand the following aesthetics (required aesthetics are in bold):

• x

• y

• group

• color

• size

• linetype

• alpha

• lineend

See Also

Other jam ggplot2 functions: gene2gg(), plotSashimi(), splicejam-extensions, to_basic.GeomShape()

Other jam ggplot2 functions: gene2gg(), plotSashimi(), splicejam-extensions, to_basic.GeomShape()

Other jam ggplot2 functions: gene2gg(), plotSashimi(), splicejam-extensions, to_basic.GeomShape()

Examples

data <- data.frame(
  x = c(1, 2, 2, 1, 2, 3, 3, 2),
  y = c(1, 2, 3, 2, 2, 1, 2, 3),
  group = c(1, 1, 1, 1, 1, 1, 1, 1)
)

ggplot(data) +
  geom_diagonal_wide_arc(aes(x, y, group=group))

# The strength control the steepness
ggplot(data, aes(x, y, group = group)) +
  geom_diagonal_wide_arc(strength=0.75, alpha=0.5, fill='red') +
  geom_diagonal_wide_arc(strength=0.25, alpha=0.5, fill='blue')

# The diagonal_wide_arc geom uses geom_shape under the hood, so corner rounding
# etc are all there
ggplot(data) +
  geom_diagonal_wide_arc(aes(x, y, group=group), radius=unit(5, 'mm'))

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.