7.2 Subnetwork visualisation

In the context of the whole/parent network (ig), visualise the gene subnetwork (subg), with 50 gene nodes labelled by gene symbols and 75 connections between nodes (network edges).

library(XGR)

## "ig" (the parent network) marked by the "subg" (the subnetwork)
ig_marked <- xMarkNet(ig, subg)

## the object "ig_marked" appended with two node attributes "xcoord" and "ycoord"
ig_marked %>% xLayout("graphlayouts.layout_with_stress") -> ig_marked

## the object "ig_marked" appended with two edge attributes
## "color" for edge coloring and "color.alpha" for edge color transparency
E(ig_marked)$color <- ifelse(E(ig_marked)$mark==0, "grey90", "cyan4")
E(ig_marked)$color.alpha <- ifelse(E(ig_marked)$mark==0, 0.1, 0.3)
V(ig_marked)$label <- ifelse(V(ig_marked)$highlight==0, '', V(ig_marked)$name)

## visualise the parent network highlighted by the subnetwork
## nodes placed by coordinates
## nodes colored differently, thus, being highlighted
## edges colored differently, thus, being highlighted
gg_marked <- ig_marked %>% xGGnetwork(node.label='label', node.label.size=2.5, node.label.color='darkblue', node.label.alpha=0.8, node.label.padding=0.1, node.label.arrow=0, node.label.force=0.01, , node.xcoord="xcoord", node.ycoord="ycoord", node.color="highlight", colormap="grey60-cyan4", node.color.alpha=0.4, node.size='highlight', node.size.range=c(0.5,2), edge.color="color", edge.color.alpha="color.alpha",edge.curve=0,edge.arrow.gap=0.01) + guides(color="none", size="none")
gg_marked

Gene subnetwork illustrated at 3 different time-points with the same layout as shown above. Nodes at each time point are coloured by log2(fold change) and sized by -log10(FDR) as indicated in the scale.

library(XGR)

## the object "subg" (subnetwork) appended with two node attributes "xcoord" and "ycoord"
ind <- match(V(subg)$name, V(ig_marked)$name)
V(subg)$xcoord <- V(ig_marked)$xcoord[ind]
V(subg)$ycoord <- V(ig_marked)$ycoord[ind]

## do visualisation
ls_subg <- lapply(seq(ncol(mat_FC)), function(j){
    g_tmp <- subg
    ind <- match(V(g_tmp)$name, rownames(mat_FC))
    V(g_tmp)$logFC <- mat_FC[ind,j]
    ind <- match(V(g_tmp)$name, rownames(mat_FDR))
    V(g_tmp)$logFDR <- -log10(mat_FDR[ind,j])
    g_tmp
})
names(ls_subg) <- colnames(mat_FC)
gg_timepoints <- xGGnetwork(ls_subg, node.label='', node.label.size=2.5, node.label.color='darkblue', node.label.alpha=0.8, node.label.padding=0.1, node.label.arrow=0, node.label.force=0.05, node.shape=19, node.xcoord='xcoord', node.ycoord='ycoord', node.color='logFC', node.color.title=expression(log[2]("FC")), colormap=c("darkblue-lightyellow-darkred",'jet.top','lightyellow-orange-darkred',"brewer.YlOrRd","ggplot2")[1], ncolors=64, zlim=c(-4,4), node.size='logFDR', node.size.title=expression(-log[10]("FDR")), node.size.range=c(0,2), slim=c(0,20), edge.color="cyan4",edge.color.alpha=0.2,edge.curve=0,edge.arrow.gap=0, title='', ncolumns=3)
gg_timepoints