xGGnetwork: Function to visualise an igraph object using ggnetwork

Description

xGGnetwork is supposed to visualise an igraph object using ggnetwork.

Usage

xGGnetwork(
g,
node.label = NULL,
label.wrap.width = NULL,
label.wrap.lineheight = 0.8,
node.label.size = NULL,
node.label.fontface = "plain",
node.label.color = "darkblue",
node.label.alpha = 0.8,
node.label.padding = 1,
node.label.arrow = 0.01,
node.label.force = 1,
node.shape = 19,
node.shape.title = NULL,
node.xcoord = NULL,
node.ycoord = NULL,
node.color = NULL,
node.color.title = NULL,
colormap = "grey-orange-darkred",
ncolors = 64,
zlim = NULL,
na.color = "grey80",
node.color.alpha = 1,
node.size = NULL,
node.size.title = NULL,
node.size.range = c(1, 4),
slim = NULL,
title = "",
edge.size = 0.5,
edge.color = "black",
edge.color.alpha = 0.5,
edge.curve = 0.1,
edge.arrow = 2,
edge.arrow.gap = 0.02,
ncolumns = NULL
)

Arguments

an object of class "igraph". For an advanced use, it can be a list of igraph objects; in this case, multiple panels will be shown (particularly useful when visualising the same network but color-coded differently)

node.label

either a vector labelling nodes or a character specifying which node attribute used for the labelling. If NULL (by default), no node labelling

label.wrap.width

a positive integer specifying wrap width of node labelling

label.wrap.lineheight

line height spacing for text in ggplot. By default it is 0.8

node.label.size

a character specifying which node attribute used for node label size

node.label.fontface

a character specifying which node attribute used for node label fontface ('plain', 'bold', 'italic', 'bold.italic')

node.label.color

a character specifying which node attribute used for the node label color

node.label.alpha

the 0-1 value specifying transparency of node labelling

node.label.padding

the padding around the labeled node

node.label.arrow

the arrow pointing to the labeled node

node.label.force

the repelling force between overlapping labels

node.shape

an integer specifying node shape or a character specifying which node attribute used for the node shape (no matter whether it is numeric or character)

node.shape.title

a character specifying the title for node shaping

node.xcoord

a vector specifying x coordinates. If NULL, it will be created using igraph::layout_as_tree

node.ycoord

a vector specifying y coordinates. If NULL, it will be created using igraph::layout_as_tree

node.color

a character specifying which node attribute used for node coloring

node.color.title

a character specifying the title for node coloring

colormap

short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta), and "ggplot2" (emulating ggplot2 default color palette). Alternatively, any hyphen-separated HTML color names, e.g. "lightyellow-orange" (by default), "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names

ncolors

the number of colors specified over the colormap

zlim

the minimum and maximum values for which colors should be plotted

na.color

the color for NAs. By default, it is 'grey80'

node.color.alpha

the 0-1 value specifying transparency of node colors

node.size

either a vector specifying node size or a character specifying which node attribute used for the node size

node.size.title

a character specifying the title for node sizing

node.size.range

the range of actual node size. Can be two values (range) or a value (fixed size)

slim

the minimum and maximum values for which sizes should be plotted

title

a character specifying the title for the plot

edge.size

a numeric value specifying the edge size. By default, it is 0.5. It can be a character specifying which edge attribute defining the edge size (though without the legend)

edge.color

a character specifying the edge color. By default, it is "black". It can be a character specifying which edge attribute defining the edge color (though

edge.color.alpha

the 0-1 value specifying transparency of edge color. By default, it is 0.5. It can be a character specifying which edge attribute defining the transparency of edge color (though without the legend)

edge.curve

a numeric value specifying the edge curve. 0 for the straight line

edge.arrow

a numeric value specifying the edge arrow. By default, it is 2

edge.arrow.gap

a gap between the arrow and the node

ncolumns

an integer specifying the number of columns for facet_wrap. By defaul, it is NULL (decided on according to the number of groups that will be visualised)

Value

a ggplot object, appended with 'data_nodes' and 'data_edges'

Examples

Run this code

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

###########################
# load REACTOME
# restricted to Immune System ('R-HSA-168256') or Signal Transduction ('R-HSA-162582')
g <- xRDataLoader(RData.customised='ig.REACTOME',
RData.location=RData.location)
neighs.out <- igraph::neighborhood(g, order=vcount(g),
nodes="R-HSA-168256", mode="out")
nodeInduced <- V(g)[unique(unlist(neighs.out))]$name
ig <- igraph::induced.subgraph(g, vids=nodeInduced)

# visualise the graph with vertices being color-coded
V(ig)$degree <- igraph::degree(ig)
gp <- xGGnetwork(g=ig, node.label='term_id', label.wrap.width=30,
node.label.size=2, node.label.color='black', node.label.alpha=0.8,
node.label.padding=0, node.label.arrow=0, node.label.force=1,
node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord',
node.color='degree', node.color.title='Degree',
colormap='grey-orange-darkred', ncolors=64, zlim=c(0,10),
node.size.range=3,
edge.color="black",edge.color.alpha=0.3,edge.curve=0.05,edge.arrow.gap=0.02,
title='')
# advanced use: visualise the list of graphs
ls_ig <- list(ig, ig)
gp <- xGGnetwork(g=ls_ig, node.label='term_id', label.wrap.width=30,
node.label.size=2, node.label.color='black', node.label.alpha=0.8,
node.label.padding=0, node.label.arrow=0, node.label.force=1,
node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord',
node.color='degree', node.color.title='Degree',
colormap='grey-orange-darkred', ncolors=64, zlim=c(0,10),
node.size.range=3,
edge.color="black",edge.color.alpha=0.3,edge.curve=0.05,edge.arrow.gap=0.02,
title='')

###########################
# load PhasedTargets
# restricted to disease ('EFO:0000408') or immune system disease ('EFO:0000540')
g <- xRDataLoader(RData.customised='ig.PhasedTargets',
RData.location=RData.location)
neighs.out <- igraph::neighborhood(g, order=vcount(g),
nodes="EFO:0000408", mode="out")
nodeInduced <- V(g)[unique(unlist(neighs.out))]$name
ig <- igraph::induced.subgraph(g, vids=nodeInduced)

# append with the number of approved and phased targets
dag <- ig
V(dag)$num_approved <- sapply(V(ig)$max_phase,function(x)
sum(x$max_phase>=4))
V(dag)$num_phased <- sapply(V(ig)$max_phase,function(x)
sum(x$max_phase>=0))
# keep nodes with num_approved >=20
dag_ig <- igraph::induced.subgraph(dag,
vids=which(V(dag)$num_approved>=20))
# (optional) further restricted to the direct children of the root
root <- dnet::dDAGroot(dag_ig)
neighs.out <- igraph::neighborhood(dag_ig, order=1, nodes=root,
mode="out")
nodeInduced <- V(dag_ig)[unique(unlist(neighs.out))]$name
dag_ig <- igraph::induced.subgraph(dag_ig, vids=nodeInduced)
# nodes colored by num_approved
V(dag_ig)$node_color <- log2(V(dag_ig)$num_approved)
glayout <- igraph::layout_with_kk(dag_ig)
V(dag_ig)$xcoord <- glayout[,1]
V(dag_ig)$ycoord <- glayout[,2]
gp <- xGGnetwork(g=dag_ig, node.label='term_name', label.wrap.width=30,
node.label.size=2, node.label.color='black', node.label.alpha=0.9,
node.label.padding=0, node.label.arrow=0, node.label.force=0.5,
node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord',
node.color='node_color', node.color.title='Approved\n(log2-scale)',
colormap='ggplot2.top', ncolors=64, node.size.range=3,
edge.color="orange",edge.color.alpha=0.5,edge.curve=0.05,edge.arrow.gap=0.02,
title='')

###########################
# visualise gene network
glayout <- igraph::layout_with_kk(g)
V(g)$xcoord <- glayout[,1]
V(g)$ycoord <- glayout[,2]
V(g)$degree <- igraph::degree(g)
gp <- xGGnetwork(g=g, node.label='name', node.label.size=2,
node.label.color='black', node.label.alpha=0.8, node.label.padding=0,
node.label.arrow=0, node.label.force=0.01, node.shape=19,
node.xcoord='xcoord', node.ycoord='ycoord', node.color='priority',
node.color.title='5-star\nrating', colormap='yellow-red', ncolors=64,
zlim=c(0,5), node.size='degree', node.size.title='Degree', slim=c(0,5),
edge.color="orange",edge.color.alpha=0.5,edge.curve=0,edge.arrow.gap=0.025,
title='')
gp_rating <- xGGnetwork(g=g, node.label='name', node.label.size=2,
node.label.color='black', node.label.alpha=0.8, node.label.padding=0.1,
node.label.arrow=0, node.label.force=0.01, node.shape=19,
node.xcoord='xcoord', node.ycoord='ycoord', node.color='priority',
node.color.title='5-star\nrating', colormap='white-yellow-red',
ncolors=64, zlim=c(0,5), node.size.range=5,
edge.color="orange",edge.color.alpha=0.3,edge.curve=0,edge.arrow.gap=0.02,
title='')

###########################
# use edge weight to color/size edges (without legends)
# edge color
#E(g)$color <- xColormap(colormap='RdYlBu', data=E(g)$weight)
#E(g)$size <- (E(g)$weight - min(E(g)$weight)) / (max(E(g)$weight) - min(E(g)$weight))
e.color <- subset(gp$data, !is.na(na.y))$e.color
gp + ggnetwork::geom_edges(color=e.color, show.legend=FALSE)
# edge size/thickness
e.size <- subset(gp$data, !is.na(na.y))$e.size
gp + ggnetwork::geom_edges(size=e.size, show.legend=FALSE)
# }

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