R 查看器窗格未显示 D3 交互式图表

Question

我在最新版本的 R 和 R studio（昨天下载）中使用 bipartiteD3 包。

当我从 bipartite_D3 函数包运行示例命令和示例文件时，它没有在查看器窗格中显示交互式二分图。相反，查看器窗格中会出现一条错误消息，指出：

d3.nest 不是函数

我附上了带有代码和错误的 R studio 页面的屏幕截图。

Answer 1

最新版本的 d3 不再包含 d3-collection 模块中包含的功能。看起来 r2D3 现在默认使用这个版本 (d3v6)，但 bipartiteD3 仍然使用它。这意味着它无法访问 d3.nest()，这解释了您的错误，因为 d3.nest 不再是 d3 的方法。

BipartiteD3 可以相对容易地更新，但同时有一些选项可以纠正这个问题，例如，您可以执行以下操作之一：

1. 安装旧版本的 r2d3 以替换当前版本

例如：

packageurl <- "https://cran.r-project.org/src/contrib/Archive/r2d3/r2d3_0.2.3.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

或

1. 在本地编辑 r 包源文件以将正确的版本传递给 r2d3（使用 d3_version = "5" 完成）

或

1. 创建一个包含所有bipartite_D3 的新函数，同时传递一个版本参数（同样使用d3_version = "5" 完成，与#2 基本相同，但不修改bipartiteD3 源）

例如：

library(r2d3)
library(bipartite )
library(purrr) 
library(dplyr) 
library(tidyr) 
library(stringr)
library(tibble)
library(RColorBrewer)
library(bipartiteD3)


testdata <- data.frame(higher = c("bee1","bee1","bee1","bee2","bee1","bee3"), 
                       lower = c("plant1","plant2","plant1","plant2","plant3","plant4"), 
                       webID = c("meadow","meadow","meadow","meadow","meadow","meadow"), freq=c(5,9,1,2,3,7))
bipartite::frame2webs(testdata)-> SmallTestWeb

Used3v5<- function(data,
                        filename='bipartiteD3Script',
                        PrimaryLab = 'Primary',
                        SecondaryLab='Secondary',
                        SiteNames=NULL,
                        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],
                        BoxLabPos = NULL,
                        IncludePerc = TRUE,
                        PercentageDecimals =0,
                        PercPos = NULL,
                        CSS_Output_Supress = FALSE,
                        PRINT=FALSE){
  df<-NULL
  
  if(tibble::is_tibble(data)){
    data<- as.data.frame(data)
  }
  
  if(is.data.frame(data)){
    df<- data
  }else{
    if(is.list(data)){
      df<-List2DF(data, PrimaryLab,SecondaryLab,SiteNames)
    }else{
      dimensions<-length(dim(data))
      if(dimensions ==3){
        df<-Array2DF(data, PrimaryLab,SecondaryLab,SiteNames)
      }
      if(dimensions==2){
        df<-Matrix2DF(data,PrimaryLab,SecondaryLab, SiteNames)
      }
    }
  }
  if(is.null(df)){#
    stop('invalid data input. Valid forms are data frame, bipartite style matrix, list or array')
  }
  
  if((mp[2]*mp[1])> (ncol(df)-2)){
    warning('Making too many facets. Are you sure mp is set ok?')
  }
  if((mp[2]*mp[1])< (ncol(df)-2)){
    warning('Making too few facets. Guessing you want 1 row')
    mp[2]<-ncol(df)-2
  }
  
  if(is.null( MainFigSize)){
    MainFigSize<-c(mp[2]*700, mp[1]*700) # Having a reasonable guess at a default overall figure size
  }
  
  BP_JS_Writer(df = df,filename = filename,
               colouroption = colouroption,
               HighlightLab = HighlightLab,
               HighlightCol = HighlightCol,
               monoChromeCol = monoChromeCol,
               ColourBy = ColourBy,
               BrewerPalette = BrewerPalette,
               NamedColourVector = NamedColourVector,
               MainFigSize = MainFigSize ,
               SortPrimary = SortPrimary,
               SortSecondary = SortSecondary,
               mp = mp,
               MinWidth = MinWidth,
               Pad = Pad,
               IndivFigSize = IndivFigSize,
               BarSize = BarSize ,
               Orientation = Orientation,
               EdgeMode = EdgeMode,
               AxisLabels= c(PrimaryLab, SecondaryLab),
               FigureLabel = SiteNames,
               BoxLabPos = BoxLabPos,
               IncludePerc = IncludePerc ,
               PercentageDecimals = PercentageDecimals,
               PercPos = PercPos,
               CSS_Output_Supress = CSS_Output_Supress ,
               PRINT =  PRINT)
  
  LoadVisJS()
  
  # only line changed here to add d3_version = "5"
  r2d3::r2d3(data = NA, d3_version="5", script = paste0(filename,".js"),
             height= MainFigSize[2], width= MainFigSize[1] ,
             dependencies ="vizjs.js")
}

Used3v5(SmallTestWeb)

Answer 2

你加载了所有的包吗？文档建议

library(r2d3)
library(bipartite)
library(purrr) 
library(dplyr) 
library(tidyr) 
library(stringr)
library(tibble)
library(RColorBrewer)
library(bipartiteD3)

https://cran.r-project.org/web//packages/bipartiteD3/vignettes/bipartiteD3_Intro.html

Answer 3

我刚刚安装了旧版本的 r2d3 (0.2.3)，它完美地显示了 R 查看器窗格中的交互式二分图。 这里我附上截图。 Here is the screenshot of R studio showing the commands and graph 谢谢@Andrew Reid