networkD3 and Shiny - filter by number of nodes

Question

I have this shiny app that generates a network graph from a df.

library(shiny)
library(dplyr)
library(tibble)
library(networkD3)

ui <- fluidPage(
  sidebarPanel(
    fluidRow(selectInput("nos","Mínimo de orientações",c(1:10),selected=c(1)))
    ),
  fluidRow(simpleNetworkOutput(
    "redes", width = "100%", height = "800px"
  ))
)
server <- function(input, output, session) {
  df_orientadores <- data.frame(orientador=c("Chet Baker","Bill Evans","Miles Davis","Miles Davis","Dizzy Gillespie","Miles Davis"),
                                autor=c("Clifford Brown","Freddie Hubbard","Kenny Dorham","Kenny Burrell","Arturo Sandoval","Goku"))
  output$redes <- renderSimpleNetwork({
    sources <- df_orientadores %>%
      select(orientador) %>%
      dplyr::rename(label = orientador)
    destination <- df_orientadores %>%
      select(autor) %>%
      dplyr::rename(label = autor)
    
    nodes <- full_join(sources, destination, by = "label")
    nodes <- nodes %>% group_by(label) %>% count(label) %>% rename(freq=n)
    
    nodes <- nodes %>% rowid_to_column("id")
    nodes$peso <- ((nodes$freq)^3)
    
    orientacoes_network <- df_orientadores %>%  
      group_by(orientador, autor) %>%
      dplyr::summarise(weight = n()) %>% 
      ungroup()
    edges <- orientacoes_network %>% 
      left_join(nodes, by = c("orientador" = "label")) %>% 
      dplyr::rename(from = id)
    
    edges <- edges %>% 
      left_join(nodes, by = c("autor" = "label")) %>% 
      dplyr::rename(to = id)
    edges <- select(edges, from, to, weight)
    nodes_d3 <- mutate(nodes, id = id - 1)
    edges_d3 <- mutate(edges, from = from - 1, to = to - 1) 
    filtro_nos <- nodes_d3
    
    edges_d3$value <- 1  
    forceNetwork(Links = edges_d3, Nodes = nodes_d3, Source = "from", Target = "to", 
                 NodeID = "label", Group = "id", Value = "value", 
                 opacity = 1, fontSize = 20, zoom = TRUE, Nodesize = "peso",
                 arrows = TRUE)
  })
}
shinyApp(ui, server)

I want to update the graph by the minimum number of nodes (described as freq in the nodes_d3 dataframe) that the user chooses (on the input$nos)

I've tried filtering the nodes_d3 and the edges_d3 by the number of frequencies but it return the error Warning: Error in $<-.data.frame: replacement has 1 row, data has 0 [No stack trace available]

any ideas how to do it?

I've tried using reactiveValues as well, but it wouldn't do. I don't know if in this kind of situation I have to subset the original dataframe and generate the network, or simply subsetting the dfs used in the forcenetwork (which I think I did but still didn't work.)

score 0 · Accepted Answer · answered Apr 12 '19 at 08:24

Once you've created your data, you need to filter both the edges_d3 and the nodes_d3 data frames, and then you need to re-adjust the from and to values in the filtered edges_d3 data frame to reflect the new positions of the nodes they refer to in the nodes_d3 data frame.

# determine the nodes that have at least the minimum freq
nodes_d3_min_freq <-
  nodes_d3 %>% 
  filter(freq >= input$nos)

# filter the edge list to contain only links to or from the nodes that have
# the minimum or more freq
edges_d3_filtered <-
  edges_d3 %>% 
  filter(from %in% nodes_d3_min_freq$id | to %in% nodes_d3_filtered$id)

# filter the nodes list to contain only nodes that are in or are linked to 
# nodes in the filtered edge list
nodes_d3_filtered <-
  nodes_d3 %>% 
  filter(id %in% unlist(select(edges_d3_filtered, from, to)))

# re-adjust the from and to values to reflect the new positions of nodes in
# the filtered nodes list
edges_d3_filtered$from <- match(edges_d3_filtered$from, nodes_d3_filtered$id) - 1
edges_d3_filtered$to <- match(edges_d3_filtered$to, nodes_d3_filtered$id) - 1

forceNetwork(Links = edges_d3_filtered, Nodes = nodes_d3_filtered, 
             Source = "from", Target = "to", NodeID = "label", 
             Group = "id", Value = "value", opacity = 1, fontSize = 20, 
             zoom = TRUE, Nodesize = "peso", arrows = TRUE)

Thanks a lot! Anyway, is there a way to edit css style from the graph? for example, the nodes border, i've tried using css but couldn't find the argument to do so. Thanks in advance. — Lucca Ramalho, Apr 16 '19 at 19:19
Not with networkD3 itself, but probably with htmlwidgets functions. Also, it would be helpful to the StackOverflow community if you mark answers as accepted if they sufficiently answer your question so that they don’t appear as unresolved. — CJ Yetman, Apr 16 '19 at 19:32

networkD3 and Shiny - filter by number of nodes

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