g6 output in Shiny stacks instead of replacing

[filipwastberg]

Hey!

Loving this new package that I feel is way more expressive and easier to configure than visNetwork that I've used the most.

However, when I want to change the underlying data in a shiny application to update the output, I noticed that the output gets stacked on the first output. I'm guessing this has to do with the htmlwidgets.

Here's a reproducible example:

library(shiny)
library(g6R)

# Module UI
network_ui <- function(id) {
  ns <- NS(id)
  tagList(
    checkboxInput(ns("filter"), "Filter Network", value = FALSE),
    g6Output(ns("network"), height = "400px")
  )
}

# Module Server
network_server <- function(id) {
  moduleServer(id, function(input, output, session) {
    get_network_data <- reactive({
      if (input$filter) {
        nodes <- data.frame(id = 1:5, label = paste("Node", 1:5))
        edges <- data.frame(source = c(1, 2, 3, 4), target = c(2, 3, 4, 5))
      } else {
        nodes <- data.frame(id = 1:10, label = paste("Node", 1:10))
        edges <- data.frame(source = c(1, 2, 3), target = c(2, 3, 4))
      }
      list(nodes = nodes, edges = edges)
    })
    
    output$network <- renderG6({
      data <- get_network_data()
      g6(data$nodes, data$edges) |>
        g6_layout(d3_force_layout())
    })
  })
}

ui <- fluidPage(network_ui("my_network"))
server <- function(input, output, session) {
  network_server("my_network")
}
shinyApp(ui, server)

The solution I found was to render the graph with renderUI and add dependency to the switch:

output$network_container <- renderUI({
  input$filter 
  g6Output(ns("network"), height = "400px")
})

Is this behavior expected? The problem arose when I tried to use g6 to replace a network in an app written with visNetwork.

Session info

> sessioninfo::session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.1 (2025-06-13)
 os       Ubuntu 24.04.2 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  sv_SE.UTF-8
 ctype    sv_SE.UTF-8
 tz       Europe/Stockholm
 date     2025-10-06
 rstudio  2025.05.1+513 Mariposa Orchid (server)
 pandoc   3.7.0.2 @ /usr/bin/pandoc
 quarto   1.7.32 @ /usr/local/bin/quarto

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────
 ! package         * version  date (UTC) lib source
 P blob              1.2.4    2023-03-17 [?] RSPM (R 4.5.0)
 P box               1.2.0    2024-02-06 [?] RSPM
 P box.linters       0.10.5   2024-09-10 [?] RSPM
 P box.lsp           0.1.3    2024-09-19 [?] RSPM
 P bsicons           0.1.2    2023-11-04 [?] RSPM (R 4.5.0)
 P bslib             0.9.0    2025-01-30 [?] RSPM
 P cachem            1.1.0    2024-05-16 [?] RSPM
 P class             7.3-23   2025-01-01 [?] CRAN (R 4.5.1)
 P classInt          0.4-11   2025-01-08 [?] RSPM (R 4.5.0)
 P cli               3.6.3    2024-06-21 [?] RSPM (R 4.5.0)
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 P fontawesome       0.5.3    2024-11-16 [?] RSPM
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 P g6R             * 0.1.0    2025-07-10 [?] RSPM
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 P glue              1.8.0    2024-09-30 [?] RSPM
 P hms               1.1.3    2023-03-21 [?] RSPM (R 4.5.0)
 P htmltools         0.5.8.1  2024-04-04 [?] RSPM
 P htmlwidgets       1.6.4    2023-12-06 [?] RSPM (R 4.5.0)
 P httpuv            1.6.15   2024-03-26 [?] RSPM (R 4.5.0)
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 P jquerylib         0.1.4    2021-04-26 [?] RSPM
 P jsonlite          1.8.9    2024-09-20 [?] RSPM (R 4.5.0)
 P KernSmooth        2.23-26  2025-01-01 [?] CRAN (R 4.5.1)
 P knitr             1.49     2024-11-08 [?] RSPM (R 4.5.0)
 P later             1.4.1    2024-11-27 [?] RSPM (R 4.5.0)
 P leaflet           2.2.3    2025-09-04 [?] RSPM
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 P purrr             1.1.0    2025-07-10 [?] RSPM
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 P Rcpp              1.0.13-1 2024-11-02 [?] RSPM (R 4.5.0)
 P reactable         0.4.4    2023-03-12 [?] RSPM (R 4.5.0)
 P reactR            0.6.1    2024-09-14 [?] RSPM (R 4.5.0)
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   renv              1.0.11   2024-10-12 [1] RSPM (R 4.5.1)
 P rhino             1.11.0   2025-04-02 [?] RSPM
 P rlang             1.1.6    2025-04-11 [?] RSPM
 P rstudioapi        0.17.1   2024-10-22 [?] RSPM
 P sass              0.4.9    2024-03-15 [?] RSPM (R 4.5.0)
 P scales            1.4.0    2025-04-24 [?] RSPM (R 4.5.0)
 P sessioninfo       1.2.3    2025-02-05 [?] RSPM (R 4.5.0)
 P sf                1.0-20   2025-03-24 [?] RSPM (R 4.5.0)
 P shiny           * 1.11.1   2025-07-03 [?] RSPM
 P shinycssloaders   1.1.0    2024-07-30 [?] RSPM (R 4.5.0)
 P shinyjs           2.1.0    2021-12-23 [?] RSPM (R 4.5.0)
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 P timechange        0.3.0    2024-01-18 [?] RSPM (R 4.5.0)
 P timevis           2.1.0    2022-11-03 [?] RSPM (R 4.5.0)
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 P units             0.8-7    2025-03-11 [?] RSPM (R 4.5.0)
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 [1] /home/user/app/renv/library/linux-ubuntu-noble/R-4.5/x86_64-pc-linux-gnu
 [2] /home/user/.cache/R/renv/sandbox/linux-ubuntu-noble/R-4.5/x86_64-pc-linux-gnu/25ebdc09

 * ── Packages attached to the search path.
 P ── Loaded and on-disk path mismatch.

────────────────────────────────────────────────────────────────────────────────────────────────────────────

[DivadNojnarg]

Hi,

Passing reactive data causes the graph to re-render that is not necessarily wanted. To change the data but not re-render the entire graph, you can use g6_set_data():

library(shiny)
library(g6R)

  
nodes <- data.frame(id = 1:5, label = paste("Node", 1:5), style = list(fill = "#CC79A7"))
edges <- data.frame(source = c(1, 2, 3, 4), target = c(2, 3, 4, 5))

# Module UI
network_ui <- function(id) {
  ns <- NS(id)
  tagList(
    actionButton(ns("update"), "Update Network"),
    g6Output(ns("network"), height = "400px")
  )
}

# Module Server
network_server <- function(id) {
  moduleServer(id, function(input, output, session) {
    ns <- session$ns
    output$network <- renderG6({
      g6(nodes, edges) |>
        g6_layout(d3_force_layout()) |>
        g6_options(
          node = list(
      style = list(
        labelBackground = TRUE,
        labelBackgroundRadius = 4,
        labelFontFamily = "Arial",
        labelPadding = c(0, 4),
        labelText = JS(
          "(d) => {
        return d.label
      }"
        )
      )
    )
        ) |>
        g6_behaviors("drag-element-force", "zoom-canvas", "drag-canvas")
    })

    observeEvent(input$update, {
    g6_proxy(ns("network")) |>
      g6_set_data(
        list(
          # Ids passed as characters: should be fixed in g6_set_data for auto conversion
          nodes = lapply(as.character(sample(1:1000, 10)), function(i) {
            list(id = i, label = paste("Node", i), style = list(fill = "#0072B2"))
          })
        )
      ) |>
      g6_fit_center()
  })
  })
}

ui <- fluidPage(network_ui("my_network"))
server <- function(input, output, session) {
  network_server("my_network")
}
shinyApp(ui, server)

I noticed however, g6_set_data has issues (my example sometimes has JS errors):

• IDs have to be converted to characters (g6 does not support numeric values). This should be done by g6_set_data like I do for g6 on initialisation.
• At the moment, you can't pass dataframes. This should be enabled like for g6.