xMarkNet: Function to mark a network within another network

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

Description

xMarkNet is supposed to mark a network within another network.

Usage

xMarkNet(ig1, ig2, verbose = TRUE)

Arguments

ig1	a "igraph" object within which the mark happens
ig2	a "igraph" object to be marked. Only overlapped nodes and edges are marked
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

an object of class "igraph" appended with a node attribute 'mark' (0 for the background, 1 for the marked) and an edge attribute 'mark' (0 for the background, 1 for the marked)

Note

none

See Also

xMarkNet

Examples

## Not run: 
# Load the library
library(XGR)

## End(Not run)

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
ig1 <- xDefineNet(network="KEGG_environmental",
RData.location=RData.location)
ig2 <- xDefineNet(network="KEGG_organismal",
RData.location=RData.location)
ig <- xMarkNet(ig1, ig2)

E(ig)$color <- ifelse(E(ig)$mark==0, 'lightblue1', 'darkgreen')
E(ig)$color.alpha <- ifelse(E(ig)$mark==0, 0.3, 0.7)
ig <- ig %>% xLayout("gplot.layout.fruchtermanreingold")
gp <- xGGnetwork(ig, node.xcoord='xcoord', node.ycoord='ycoord',
node.color="mark", colormap="orange-darkgreen", node.color.alpha=0.7,
edge.color="color", edge.color.alpha="color.alpha", edge.arrow.gap=0) +
theme(legend.position='none')

## End(Not run)

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