BP_JS_Writer {bipartiteD3}

Generate JavaScript file for a bipartite network

Description

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

Usage

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?

Value

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')