getVNPlotObject function

getVNPlotObject

uses visNetwork to produce an interactive network plot based on the links and edges dataframes

getVNPlotObject(
  nodes,
  edges,
  addLegend = FALSE,
  addExport = TRUE,
  figType = "png",
  mainTitle = NULL,
  subTitle = NULL,
  layoutSeed = NA,
  scaleNodes = FALSE,
  scaleEdges = FALSE,
  microbeCol = "gold",
  resourceCol = "lightblue",
  productionCol = "magenta",
  uptakeCol = "darkgrey",
  figWidth = 700,
  figHeight = 700
)

Arguments

• nodes: data frame or a list with nodes information. Needs at least column "id". See visNetwork::visNodes
• edges: data frame or a list with edges information. Needs at least columns "from" and "to". See visNetwork::visEdges
• addLegend: Logical. If true adds a legend to plot. Default is FALSE
• addExport: Logical. If true adds button to export fig from html plot
• figType: Type of export. One of "png" (default), "jpeg" or "pdf". Puts a button on the html plot
• mainTitle: Optional list containing "text" (string for plot title) and "style" (e.g. 'font-family:Times','font-family:Arial' etc).
• subTitle: Optional list containing "text" (string for plot subtitle) and "style" (e.g. 'font-family:Times','font-family:Arial' etc)
• layoutSeed: : NA. Random seed for the layout of the plot. To get identical plots set this to a number
• scaleNodes: Logical. If true the node sizes differ with concentration (in moles for resources and mass or concentration for microbes)
• scaleEdges: Logical. If true the edge sizes differ with the amount of moles flowing through them
• microbeCol: String for microbe node colour. Default is 'orange'
• resourceCol: String for resource node colour. Default is 'lightBlue'
• productionCol: String for production edge colour. Default is 'darkGrey'
• uptakeCol: String for uptake edge colour. Default is 'magenta'
• figWidth: numeric value to control size of plotting window. Default is 700
• figHeight: numeric value to control size of plotting window. Default is 700

Returns

a visNetwork object that can be shown using print() function.