xA2Net: Function to visualise an igraph object in a ggplot style
In A2: Atlas and Analysis of Systems-Biology-Led Pathways

Description Usage Arguments Value Note See Also Examples

View source: R/xA2Net.r

xA2Net is supposed to visualise an igraph object in a ggplot style.

xA2Net(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.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)

`g`	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_with_kk
`node.ycoord`	a vector specifying y coordinates. If NULL, it will be created using igraph::layout_with_kk
`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.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
`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
`edge.color`	a character specifying which edge attribute defining the the edge colors
`edge.color.alpha`	the 0-1 value specifying transparency of edge colors
`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

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

none

xA2Net

# Load the library
library(A2)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev/"

## Not run: 
# 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 <- xA2Net(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 <- xA2Net(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='')

###########################
# 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 <- xA2Net(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 <- xA2Net(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='')

## End(Not run)