annotateGraph: Annotate NetBox graph
In netboxr: netboxr

Description Usage Arguments Details Value Author(s) Examples

View source: R/annotateGraph.R

This function annotates the graph based on user input.

annotateGraph(
  netboxResults,
  edgeColors = NULL,
  directed = FALSE,
  linker = TRUE
)

`netboxResults`	Output from `geneConnector` function. a list of returned netboxr results netboxGraph: igraph object of NetBox algorithm identified network nodes and connections netboxCommunity: igraph object of network community assignment netboxOutput: data frame of NetBox algorithm identified network nodes and connections nodeType: data frame of node types ("candidate" or "linker") in the NetBox algorithm indentified network. moduleMembership: data frame of module (community) membership. neighborData: data frame of information of nodes directly connected to candidate gene nodes.
`edgeColors`	table containing hex color codes for interaction types. The first column is interaction type and the second column is hex color code.
`directed`	boolean value indicating whether the NetBox algorithm identified network is directed or undirected (default = FALSE)
`linker`	boolean value indicating whether "linker" nodes exist in the NetBox algorithm identified network or not (default = TRUE)

If a table of color codes for interaction types is provided, then the edges will be colored accordingly by interaction types. If directed is TRUE, then the edges will be arrows with the same directionality as the original input network for NetBox. If linker is TRUE, then linker nodes will be shown as squares while non-linker nodes stay as circles.

annotated version of netboxGraph

Guanlan Dong, guanlan_dong@g.harvard.edu

data(pathway_commons_v8_reactome)
interaction_type_color <- read.csv(system.file("interaction_type.color.txt", package = "netboxr"),
                                   header=TRUE, sep="\t", stringsAsFactors=FALSE)

sifNetwork<-pathway_commons_v8_reactome$network
graphReduced <- networkSimplify(sifNetwork,directed = FALSE)

geneList <- pathway_commons_v8_reactome$geneList

results <- geneConnector(geneList = geneList, networkGraph = graphReduced, 
                         directed = FALSE, pValueAdj = "BH", pValueCutoff = 2e-5, 
                         communityMethod = "ebc", keepIsolatedNodes = FALSE)

netboxGraphAnnotated <- annotateGraph(netboxResults = results,
                                      edgeColors = interaction_type_color,
                                      directed = TRUE,
                                      linker = TRUE)

# As an example, plot both the original and the annotated graphs
ll <- layout_with_fr(results$netboxGraph) # Save the layout for easier comparison
# Plot original graph
pdf("originalGraph.pdf", width = 50, height = 50)
plot(results$netboxCommunity, results$netboxGraph, layout = ll,
     vertex.size=3)
dev.off()
# Plot annotated graph
pdf("annotatedGraph.pdf", width = 50, height = 50)
plot(results$netboxCommunity, netboxGraphAnnotated, layout = ll,
     vertex.size = 3,
     vertex.shape = V(netboxGraphAnnotated)$shape,
     edge.color = E(netboxGraphAnnotated)$interactionColor,
     edge.width = 3)
# Add legend
ind <- which(interaction_type_color$INTERACTION_TYPE %in% E(netboxGraphAnnotated)$interaction)
legend_interaction_type <- interaction_type_color$INTERACTION_TYPE[ind]
legend_interaction_type_color <- interaction_type_color$COLOR[ind]
legend(x=-1.1, y=1.1, 
       legend=c("Candidate", "Linker"),
       pch=c(19, 15), # solid circle, filled square
       pt.cex = 8,
       bty="n",
       title="Node Types",
       cex=4, ncol=1)
legend(x=-1.15, y=0.95, 
       legend=legend_interaction_type,
       col = legend_interaction_type_color,
       lty = 1, lwd = 10,
       bty="n",
       title="Interaction Types (Edges)",
       cex=4, ncol=1)
dev.off()