annotateGraph {netboxr} | R Documentation

## Annotate NetBox graph

### Description

This function annotates the graph based on user input.

### Usage

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

### Arguments

`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)

### Details

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.

### Value

annotated version of netboxGraph

### Author(s)

Guanlan Dong, guanlan_dong@g.harvard.edu

### Examples

    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()

[Package netboxr version 1.7.1 Index]