BP_JS_Writer function

Generate JavaScript file for a bipartite network

Function called by bipartite_D3() to write JavaScript and CSS file. In most cases it is better to use bipartite_D3() directly.

BP_JS_Writer(
  df,
  filename = "JSBP",
  colouroption = c("monochrome", "brewer", "manual")[1],
  HighlightLab = "Unlinked",
  HighlightCol = "#3366CC",
  monoChromeCol = "rgb(56,43,61)",
  ColourBy = c(1, 2)[2],
  BrewerPalette = "Accent",
  NamedColourVector,
  MainFigSize = NULL,
  SortPrimary = NULL,
  SortSecondary = NULL,
  mp = c(1, 1),
  MinWidth = 10,
  Pad = 1,
  IndivFigSize = c(200, 400),
  BarSize = 35,
  Orientation = c("vertical", "horizontal")[1],
  EdgeMode = c("straight", "smooth")[2],
  AxisLabels = NULL,
  FigureLabel = NULL,
  BoxLabPos = NULL,
  IncludePerc = TRUE,
  PercentageDecimals = 0,
  PercPos = NULL,
  CSS_Output_Supress = FALSE,
  PRINT = FALSE
)

Arguments

• df: data.frame containing the names of the interactors and the link strengths. bipartite package data need to be passed through Matrix2DF or Array2DF first.
• filename: character string to name the .js and .css files. Do not include a file extension
• colouroption: Either 'monochrome', 'brewer' or 'manual'
• HighlightLab: Name of interactor to highlight
• HighlightCol: Highlight colour
• monoChromeCol: If using monochrome option, what colour to use
• ColourBy: Which set of interactors to colour by. 1= primary, 2= secondary
• BrewerPalette: RColorBrewer palette
• NamedColourVector: Named vector of colours for manual colour assignment
• MainFigSize: Size of figure, used here to calculate facet spacing.
• SortPrimary: Vector detailing order to arrange primary level. Default is alphabetical
• SortSecondary: Vector detailing order to arrange secondary level. Default is alphabetical
• mp: Numeric vector c(rows, columns)
• MinWidth: Numeric. Minimum size to shrink unselected interactors to.
• Pad: Numeric. Gap between species.
• IndivFigSize: Size of each facet, specifically the interactions.
• BarSize: Thickness of bars representing interactors
• Orientation: Either 'horizontal' or 'vertical' orientation.
• EdgeMode: Set to 'straight' to avoid curly lines.
• AxisLabels: c('Primary','Secondary') to overide column names of dataframe
• FigureLabel: Character vector, to allow overide of use of df column names
• BoxLabPos: c(x_p,x_s) To adjust position of species labels. Default is based on maximum length of labels.
• IncludePerc: Boolean. whether or not to show percentage links
• PercentageDecimals: Number of decimal places to display percentages to. Useful if rare species are rounded to 0.
• PercPos: c(x_p,x_s) To adjust position of percentages. Default is based on maximum length of labels.
• CSS_Output_Supress: Boolean. Set to TRUE if you have changed the CSS file manually and don't want it over written
• PRINT: Boolean. Output generated JavaScript to screen?

Returns

As a side effect, saves visjs.js (vis plotting library), filename.js and filename.css to the working directory.

Examples

## Simple Data Set
testdata <- data.frame(higher = c("bee1","bee1","bee1","bee2","bee1","bee3"),
lower = c("plant1","plant2","plant1","plant2","plant3","plant4"),
 Meadow=c(5,9,1,2,3,7))

BP_JS_Writer(testdata,PRINT=TRUE)

## tidy up (to keep CRAN happy, not needed in real life use)
file.remove('vizjs.js')
file.remove('JSBP.js')
file.remove('JSBP.css')