XGR (version 1.1.7)

xGGraph: Function to visualise an igraph object using ggraph

Description

xGGraph is supposed to visualise an igraph object using ggraph, with nodes/tips labelled (aligned to left-right or top-bottom edges).

Usage

xGGraph(
ig,
layout = "partition",
circular = T,
leave = T,
node.label.size = 2,
node.label.direction = c("none", "leftright", "topbottom"),
node.label.color = "steelblue",
node.label.alpha = 0.7,
node.label.wrap = NULL,
node.label.offset = 0.5,
node.size = 2,
limit.expansion = NULL,
edge = c("diagonal", "link", "arc", "fan", "elbow"),
edge.color = "grey",
edge.alpha = 0.5,
edge.width = 0.5,
...
)

Arguments

ig

an object of class "igraph" with node attribute 'name'. It could be a 'phylo' object converted to. Note: the node/leave labels would be the node attribute 'name' unless the node attribute 'label' is explicitely provided

layout

the layout supported in ggraph::create_layout. This can be ggraph layouts 'partition' (by default), 'dendrogram', 'circlepack', 'treemap' (-1,1). This can be also igraph-supported layout ('nicely','fr','kk','sugiyama','randomly','star','circle','gem','dh','graphopt','grid','mds','drl','lgl','sphere')

circular

the logic specifying whether or not circular representations. This will be disabled implicitly if the layout does not support circularity

leave

the logic specifying whether or not only leaves (nodes/labellings) shown. This can be disenabled if the layout does not support tips

node.label.size

the text size of the leave labelings. By default, it is 2. If 0, all labellings will be disabled

node.label.direction

the leave label direction. It can be "none", "leftright" (aligned to the left- and right-most edge) and "topbottom" (aligned to the top- and bottom-most edge)

node.label.color

the color of the leave labelings

node.label.alpha

the alpha of the leave labelings

node.label.wrap

the wrap width of the leave labelings

node.label.offset

the offset of the leave labelings aligned to the edge. It is defined as relative to the range of limits (x-limit for left-right, and y-limit for top-bottom)

node.size

the size of the leave nodes. By default, it is 0

limit.expansion

the x- and y-limit expansion. By default, it is NULL, decided by "node.label.offset"

edge

the edge type. It can be "diagonal" (default) , "link" (straight lines), "arc", "fan" (curves of different curvature), "elbow"

edge.color

the color of edges

edge.alpha

the alpha of edges

edge.width

the width of edges

...

additional graphic parameters (such as size, color) used in ggrepel::geom_text_repel to control labels

Value

a ggplot2 object appended with 'ig' and 'data' which should contain columns 'x','y','name' (the same as V(ig)$name), 'label' (if not given in ig, a 'name' varient). Also contain 'leaf' (T/F), 'depth' (the number of step to the root) for tree-like graph with certain layouts.

See Also

xGGraph

Examples

# NOT RUN {
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"

AA.template <- xRDataLoader("AA.template",
RData.location=RData.location)
# consensus tree
ig <- AA.template$consensus$ig

# Default: partition-like circular layout
# none
gp <- xGGraph(ig, node.label.direction="none", node.label.wrap=50)
# leftright
gp <- xGGraph(ig, node.label.direction="leftright", node.label.wrap=50,
node.label.offset=0.5)
# topbottom
gp <- xGGraph(ig, node.label.direction="topbottom", node.label.wrap=50,
node.label.offset=0.5)

# advanced usage
## ggraph layouts
gp <- xGGraph(ig, layout='dendrogram',
node.label.direction="leftright")
gp <- xGGraph(ig, layout='treemap')
gp <- xGGraph(ig, layout='circlepack')
## igraph layouts
set.seed(825)
gp <- xGGraph(ig, layout='nicely', node.label.direction="leftright")
gp <- xGGraph(ig, layout='kk')
gp <- xGGraph(ig, layout='fr', node.label.direction="leftright")
gp <- xGGraph(ig, layout='gem')
# }