xGraphML: Function to generate a graphml file from a graph object of...

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

Description

xGraphML is supposed to generate a graphml file from a graph object of class "igraph".

Usage

xGraphML(
g,
node.label = NULL,
label.wrap.width = NULL,
node.label.size = 12,
node.label.color = "#000000",
node.tooltip = NULL,
node.link = NULL,
node.xcoord = "xcoord",
node.ycoord = "ycoord",
node.color.na = "#dddddd",
node.color = NULL,
colormap = "grey-orange-darkred",
ncolors = 64,
nlegend = 11,
legend.label.size = 10,
legend.interval = 0.05,
zlim = NULL,
node.size = 30,
node.coord.scale = 300,
edge.color = "#00000033",
edge.width = 1,
filename = "xGraphML",
verbose = T
)

Arguments

g	an object of class "igraph"
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. If provided as a vector, a node with 'NA' will be not labelled
label.wrap.width	a positive integer specifying wrap width of name
node.label.size	the node label size
node.label.color	the node label color
node.tooltip	either a vector used for node tooltips or a character specifying which node attribute used for the tooltips. If NULL (by default), node attribute 'name' will be used node lab
node.link	either a vector used for node link or a character specifying which node attribute used for the link
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.na	the color for nodes with NA. By default, it is '#dddddd'
node.color	a character specifying which node attribute used for node coloring. If NULL (by default), it is '#BFFFBF'
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
nlegend	the number of colors specified in the legend. By default, it is 11
legend.label.size	the legend label size. By default, it is 10
legend.interval	the interval between legends. By default, it is 0.05
zlim	the minimum and maximum z/patttern values for which colors should be plotted, defaulting to the range of the finite values of z. Each of the given colors will be used to color an equispaced interval of this range. The midpoints of the intervals cover the range, so that values just outside the range will be plotted
node.size	either a vector specifying node size or a character specifying which node attribute used for the node size. If NULL (by default), it will be 30
node.coord.scale	the node coord (-1,1) subjected to be rescaled. By default, it is 300
edge.color	a character specifying the edge colors. By default, it is #00000033
edge.width	the edge width. By default, it is 1
filename	the without-extension part of the name of the output file. By default, it is 'xGraphML'
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

invisible (a string storing graphml-formatted content). If the filename is not NULL, a graphml-formatted file is also output.

Note

none

See Also

xGraphML

Examples

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

# 1) load REACTOME
# 1a) 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))]$name
ig <- igraph::induced.subgraph(g, vids=nodeInduced)
# visualise the graph with vertices being color-coded by the pattern
V(ig)$pattern <- runif(vcount(ig))
xGraphML(g=ig, node.label="name", node.color="pattern", colormap="wyr",
node.size=10, node.label.size=6)

# 1b) restricted to 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-162582", mode="out")
nodeInduced <- V(g)[unique(unlist(neighs.out))]$name
ig <- igraph::induced.subgraph(g, vids=nodeInduced)
# visualise the graph with vertices being color-coded by the pattern
V(ig)$pattern <- runif(vcount(ig))
xGraphML(g=ig, node.label="name", node.color="pattern", colormap="wyr",
node.size=8, node.label.size=4)

###########################
# visualise gene network
glayout <- igraph::layout_with_kk(ig)
V(ig)$xcoord <- glayout[,1]
V(ig)$ycoord <- glayout[,2]
V(ig)$node.link <-
paste0("http://www.genecards.org/cgi-bin/carddisp.pl?gene=",
V(ig)$name)
xGraphML(g=ig, node.label="name", node.tooltip="description",
node.xcoord="xcoord", node.ycoord="ycoord", node.color="pattern",
colormap="grey-orange-darkred", node.link="node.link", nlegend=11,
node.size=30, node.coord.scale=300)

## End(Not run)

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