D3heatmap and networkD3 not working together

[Ewelina Sowka]

Hello.

When I try to render on one of shiny dashboard pages d3heatmap it is not working with networkD3 possibly rendering on another page. When I comment network heatmap is working. Could you please help me to solve this problem?

[Aline Deschamps]

Hello,

I'm not sure without seeing your code but may be it could be something linked to default id for d3heatmap and networkD3 viz ?

If you have two d3heatmap in your app (and no networkD3 or a commented networkD3), is it still working ?

HTH ! :)

Best regards.

-- Aline

[Ewelina Sowka]

Hello

It seems not to be working with 2 heatmaps. I would be really greatfull if you could help.

Code for the heatmap and network:

ui.R

tabItem(tabName = "heatMap",

              h2("Heat Map"),

              fluidRow(

                box(

                  width=3,

                  # collapsible = TRUE,

                  conditionalPanel(

                    condition = "input.goButton == true",

                    uiOutput("heatmapOptions1"),

                    conditionalPanel(

                      condition = "input.statisticalCriterion != null",

                      uiOutput("heatmapOptions2"),

                      actionButton("goButtonHeat", "Draw Heatmap"))

                  )),

                box(width=9,

                    uiOutput("pixelation"))

                ))

tabItem(tabName = "network",

        h2("Network Analysis"),

        fluidRow(

          box(width = 12,

              conditionalPanel(

                condition = "input.goData == true",

                actionButton("doNets", "Do Network Analysis")

                # ,

                # downloadButton("downloadSimpleNetwork", "Download Network")

              ))

          ,

          box(width = 12,

              simpleNetworkOutput("networkData", width= "100%", height="500px"))

          )

        )

server.R

# heatmap height

  output$pixelation <- renderUI({

    d3heatmapOutput("heatmap",

                    width = "100%",

                    height = "700px")

    })

  

  # log2 data transformation

  log2_datasetInput <- reactive({

    cpm(slimStats(), prior.count=2, log=TRUE)

  })

  

  output$heatmap <- d3heatmap::renderD3heatmap({

    validate(need(input$goButtonHeat !=0 , "To create a heatmap showing statistically significant genes, first perform differential expression analysis and then specify your parameters and press 'Draw Heatmap' button"))

    if(input$log2_transformed_data){dataset<-log2_datasetInput()}else{dataset<-slimStats()}

    d3heatmap(

        dataset,

        cexRow = as.numeric(as.character(input$xfontsize)),

        cexCol = as.numeric(as.character(input$yfontsize)),

        colors = colorRampPalette(c("red", "yellow", "green"))(n = input$numberOfInterestingGenes),

        k_row = input$color_row_branches,

        k_col = input$color_column_branches,

        dendrogram = input$dendrogram

      )

  })

# simple network engine prep

  grow <- function(nominal_GO_df, rownamespwfOne, enriched.GO, Genome, topEnriched) ({

    total = list()

    getGo <- getgo(rownamespwfOne, Genome, input$geneRef)

    Base = data.table(rownamespwfOne, getGo)

    for(go in nominal_GO_df$ind[1:topEnriched]){

      Names <- Base$rownamespwfOne[grep(go,Base$getGo)]

      nameList = list(Names) 

      total = append(total, nameList)

    }

    names(total) <- nominal_GO_df$ind[1:topEnriched]

    total <- total

  })

  # simple network engine

  network <- reactive({

    enriched.GO <- enriched()

    #network analysis loop (FDR vs nominal p-value) within simple network engine

    if(!length(enriched.GO) == 0){

      nominal_GO_df <- stack(lapply(mget(enriched.GO, GOTERM, ifnotfound = NA), Term)) 

      

      total <- grow(nominal_GO_df, rownamespwfOne, input$chooseEnriched, input$Genome, input$numberGenes)

      namesGo <- names(total)

      vector = c()

      targetVector = c()

      

      for (go in 1:length(namesGo)){

        lengthName <- length(total[[go]])

        for(populate in 1:lengthName){

          nameGene <- nominal_GO_df$values[grep(namesGo[go], nominal_GO_df$ind)]

          vector = append(vector, nameGene)

          targetVector = append(targetVector, total[[go]][populate])

        }

      }

      src <- vector

      target <- targetVector

      networkData <- data.frame(src, target)   

      simpleNetwork(networkData)

                    # , charge = -1000, opacity = 1, zoom = T)

    }

    else {

      return(validate(need(input$goData == 0, "No enriched genes are available to make a network at this statistical cutoff level")))

    }

  })

  

  # simple network output

  output$networkData <- renderSimpleNetwork({

    if (input$doNets == 0) {return(validate(

      need(input$countMatrix != 0, "For network analysis, please first select a file for input") %then%

        need(input$goButton != 0, "For network analysis, please first perform Differential Expression Analysis") %then%

        need(input$goData != 0, "For network analysis, please perform Gene Ontology analysis") %then%

        need(input$doNets != 0, "For network analysis, please click on 'Do Network Analysis' and wait for about 5-30 seconds")

    ))}

    else {

      network()

    }

  })

})

This are just the parts of code but it was too much to copy everything. 

Thank You.

[Joe Cheng]

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[Ewelina Sowka]

I just have noticed it:

Uncaught TypeError: xaxis.style is not a function

    at eval (eval at <anonymous> (jquery.min.js:2), <anonymous>:194:11)

    at heatmap (eval at <anonymous> (jquery.min.js:2), <anonymous>:214:5)

    at eval (eval at <anonymous> (jquery.min.js:2), <anonymous>:58:16)

    at Image.img.onload (eval at <anonymous> (jquery.min.js:2), <anonymous>:110:7)

[Amanda Mason-Singh]

Hello Ewelina!

I am having this same issue when using both the networkD3 package and the d3heatmap package to plot different figures on the same R Shiny app.

See this issue here: https://github.com/rstudio/d3heatmap/issues/77

It looks like the problem is likely due to d3heatmap using an older version of D3.js, while networkD3 uses (presumably) a never version of D3.js.

I have left a comment on the github page for d3heatmap to see if the issue will be resolved.

If you were able to solve your problem another way, please share.  :)

Best,

Amanda