geom_edge_elbow: Draw edges as elbows

Description

This geom draws edges as an angle in the same manner as known from classic dendrogram plots of hierarchical clustering results. In case a circular transformation has been applied the first line segment will be drawn as an arc as expected. This geom is only applicable to layouts that return a direction for the edges (currently layout_tbl_graph_dendrogram(), layout_tbl_graph_partition() and layout_tbl_graph_igraph() with the "tree" algorithm).

Usage

geom_edge_elbow(
  mapping = NULL,
  data = get_edges(),
  position = "identity",
  arrow = NULL,
  strength = 1,
  flipped = FALSE,
  n = 100,
  lineend = "butt",
  linejoin = "round",
  linemitre = 1,
  label_colour = "black",
  label_alpha = 1,
  label_parse = FALSE,
  check_overlap = FALSE,
  angle_calc = "rot",
  force_flip = TRUE,
  label_dodge = NULL,
  label_push = NULL,
  show.legend = NA,
  ...
)
geom_edge_elbow2(
  mapping = NULL,
  data = get_edges("long"),
  position = "identity",
  arrow = NULL,
  strength = 1,
  flipped = FALSE,
  n = 100,
  lineend = "butt",
  linejoin = "round",
  linemitre = 1,
  label_colour = "black",
  label_alpha = 1,
  label_parse = FALSE,
  check_overlap = FALSE,
  angle_calc = "rot",
  force_flip = TRUE,
  label_dodge = NULL,
  label_push = NULL,
  show.legend = NA,
  ...
)
geom_edge_elbow0(
  mapping = NULL,
  data = get_edges(),
  position = "identity",
  arrow = NULL,
  flipped = FALSE,
  lineend = "butt",
  show.legend = NA,
  ...
)

Arguments

mapping: Set of aesthetic mappings created by ggplot2::aes() or ggplot2::aes_(). By default x, y, xend, yend, group and circular are mapped to x, y, xend, yend, edge.id and circular in the edge data.
data: The return of a call to get_edges() or a data.frame giving edges in correct format (see details for for guidance on the format). See get_edges() for more details on edge extraction.
position: Position adjustment, either as a string, or the result of a call to a position adjustment function.
arrow: Arrow specification, as created by grid::arrow().
strength: How bend the elbow should be. 1 will give a right angle, while 0 will give a straight line. Ignored for circular layouts
flipped: Logical, Has the layout been flipped by reassigning the mapping of x, y etc?
n: The number of points to create along the path.
lineend: Line end style (round, butt, square).
linejoin: Line join style (round, mitre, bevel).
linemitre: Line mitre limit (number greater than 1).
label_colour: The colour of the edge label. If NA it will use the colour of the edge.
label_alpha: The opacity of the edge label. If NA it will use the opacity of the edge.
label_parse: If TRUE, the labels will be parsed into expressions and displayed as described in grDevices::plotmath().
check_overlap: If TRUE, text that overlaps previous text in the same layer will not be plotted. check_overlap happens at draw time and in the order of the data. Therefore data should be arranged by the label column before calling geom_text(). Note that this argument is not supported by geom_label().
angle_calc: Either 'none', 'along', or 'across'. If 'none' the label will use the angle aesthetic of the geom. If 'along' The label will be written along the edge direction. If 'across' the label will be written across the edge direction.
force_flip: Logical. If angle_calc is either 'along' or 'across' should the label be flipped if it is on it's head. Default to TRUE.
label_dodge: A grid::unit() giving a fixed vertical shift to add to the label in case of angle_calc is either 'along' or 'across'
label_push: A grid::unit() giving a fixed horizontal shift to add to the label in case of angle_calc is either 'along' or 'across'
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.
...: 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.

Aesthetics

geom_edge_elbow and geom_edge_elbow0 understand the following aesthetics. Bold aesthetics are automatically set, but can be overridden.

x
y
xend
yend
circular
direction
edge_colour
edge_width
edge_linetype
edge_alpha
filter

geom_edge_elbow2 understand the following aesthetics. Bold aesthetics are automatically set, but can be overridden.

x
y
group
circular
direction
edge_colour
edge_width
edge_linetype
edge_alpha
filter

geom_edge_elbow and geom_edge_elbow2 furthermore takes the following aesthetics.

start_cap
end_cap
label
label_pos
label_size
angle
hjust
vjust
family
fontface
lineheight

Computed variables

index: The position along the path (not computed for the *0 version)

Edge variants

Many geom_edge_* layers comes in 3 flavors depending on the level of control needed over the drawing. The default (no numeric postfix) generate a number of points (n) along the edge and draws it as a path. Each point along the line has a numeric value associated with it giving the position along the path, and it is therefore possible to show the direction of the edge by mapping to this e.g. colour = stat(index). The version postfixed with a "2" uses the "long" edge format (see get_edges()) and makes it possible to interpolate node parameter between the start and end node along the edge. It is considerable less performant so should only be used if this is needed. The version postfixed with a "0" draws the edge in the most performant way, often directly using an appropriate grob from the grid package, but does not allow for gradients along the edge.

Often it is beneficial to stop the drawing of the edge before it reaches the node, for instance in cases where an arrow should be drawn and the arrowhead shouldn't lay on top or below the node point. geom_edge_* and geom_edge_*2 supports this through the start_cap and end_cap aesthetics that takes a geometry() specification and dynamically caps the termini of the edges based on the given specifications. This means that if end_cap = circle(1, 'cm') the edges will end at a distance of 1cm even during resizing of the plot window.

All geom_edge_* and geom_edge_*2 have the ability to draw a label along the edge. The reason this is not a separate geom is that in order for the label to know the location of the edge it needs to know the edge type etc. Labels are drawn by providing a label aesthetic. The label_pos can be used to specify where along the edge it should be drawn by supplying a number between 0 and 1. The label_size aesthetic can be used to control the size of the label. Often it is needed to have the label written along the direction of the edge, but since the actual angle is dependent on the plot dimensions this cannot be calculated beforehand. Using the angle_calc argument allows you to specify whether to use the supplied angle aesthetic or whether to draw the label along or across the edge.

Edge aesthetic name expansion

In order to avoid excessive typing edge aesthetic names are automatically expanded. Because of this it is not necessary to write edge_colour within the aes() call as colour will automatically be renamed appropriately.

Author

Thomas Lin Pedersen

Examples

Run this code

require(tidygraph)
irisDen <- hclust(dist(iris[1:4], method = 'euclidean'), method = 'ward.D2') %>%
  as_tbl_graph() %>%
  mutate(class = sample(letters[1:3], n(), TRUE)) %>%
  activate(edges) %>%
  mutate(class = sample(letters[1:3], n(), TRUE))

ggraph(irisDen, 'dendrogram', circular = TRUE) +
  geom_edge_elbow(aes(alpha = stat(index)))

ggraph(irisDen, 'dendrogram') +
  geom_edge_elbow2(aes(colour = node.class))

ggraph(irisDen, 'dendrogram', height = height) +
  geom_edge_elbow0(aes(colour = class))

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