BP_JS_Writer: Generate JavaScript file for a bipartite network

In bipartiteD3: Interactive Bipartite Graphs

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')

bipartiteD3 documentation built on Sept. 11, 2024, 7:25 p.m.