xGGraph: Function to visualise an igraph object using ggraph

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

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.

Note

none

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')

## End(Not run)

XGR documentation built on Jan. 8, 2020, 5:06 p.m.