Network diagrams (also called Graphs) show interconnections between a set of entities. Each entity is represented by a Node (or vertice). Connection between nodes are represented through links (or edges). Networks is an entire field of research in itself. For example, you need to set up a layout algorythm that finds out an optimal position for each node. Several type of networks exist. They can be directed (flow) or undirected (connection). Links can be wheigthed or not.
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60, "x" : 860, "y" : 560, "zorder" : "32952" }, { "color" : "rgba(0,0,0,0)", "database" : "Ensembl : ENSG00000276752", "fontsize" : "10", "graphid" : "d53a2", "groupref" : "d254c", "height" : 20, "hiddenParent" : false, "id" : "d53a2", "label" : "MIR29B2", "labelColor" : "rgb(153,0,153)", "labelSize" : 1, "labelXi" : 395.3, "labelYi" : 473.7, "nodeName" : "datanode", "outline" : "rgb(153,0,153)", "parentNode" : "d254c", "shape" : "rectangle", "type" : "GeneProduct", "valign" : "Middle", "width" : 61, "x" : 395.3, "y" : 473.7, "zorder" : "32955" }, { "color" : "rgba(0,0,0,0)", "eventless" : true, "height" : 1, "hideLabel" : true, "hideTooltip" : false, "id" : "d5f68", "label" : "", "labelSize" : 1, "outline" : "rgba(0,0,0,0)", "shape" : "circle", "type" : "Anchor", "width" : 1, "x" : 879.6, "y" : 216.5, "zorder" : 0 }, { "color" : "rgba(0,0,0,0)", "eventless" : true, "height" : 1, "hideLabel" : true, "hideTooltip" : false, "id" : "cac70", "label" : "", "labelSize" : 1, "outline" : "rgba(0,0,0,0)", "shape" : "circle", "type" : "Anchor", "width" : 1, "x" : 397.5, "y" : 173.1, "zorder" : 0 } ] } <-- Create the configuration for the graph --> var config = { "adjustBezier":"false", "calculateLayout":"false", "colorNodeBy":"Exp1", "graphType":"Network", "networkFreeze":"true", "networkNodesOnTop":"false", "preScaleNetwork":"false", "showNodeNameThreshold":"20000", "title":"Apoptosis" } <!-- Call the CanvasXpress function to create the graph --> var cX = new CanvasXpress("canvasId", data, config); </script>
library(canvasXpress) nodes=read.table("https://www.canvasxpress.org/data/cX-wpapoptosis-nodes.txt", header=TRUE, sep="\t", quote="", fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE) edges=read.table("https://www.canvasxpress.org/data/cX-wpapoptosis-edges.txt", header=TRUE, sep="\t", quote="", fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE) canvasXpress( nodeData=nodes, edgeData=edges, adjustBezier=FALSE, calculateLayout=FALSE, colorNodeBy="Exp1", graphType="Network", networkFreeze=TRUE, networkNodesOnTop=FALSE, preScaleNetwork=FALSE, showNodeNameThreshold=20000, title="Apoptosis" )