Zero-index problem and filtering issue in shiny

Question

I am trying to build a shiny app with an interactive network, but I am stuck with two problems.

Firstly, I cannot figure out why I do have problem with zero indexing, because I used the solution to fix it, but it does not work properly. On the other hand, I do something wrong maybe.

Secondly, I have an issue with filtering the nodes based on the group (list_initiators$factions). Currently, the graph reacts when I want to change “connections”, but it has some malfunctions with factions. I want the graph to display only nodes from factions, which do have the connections. When I untick some factions in sidebox, the graph freezes when there is no connections and it doesn't react properly. You can see that in a table as well.

Here is my code

library(shiny)
library(dplyr)
library(tidyr)
library(networkD3)

list_initiators <- read.csv("https://raw.githubusercontent.com/Okssana/shiny_app_network/master/nodes_amends_20_09_2020.csv", fileEncoding = "Windows-1251") %>%
  select(-X)

edges_for_gephy <- read.csv("https://raw.githubusercontent.com/Okssana/shiny_app_network/master/edges_amends_20_09_2020.csv") %>% 
  select(-X)


# UI ####
ui <- fluidPage(
  
  sidebarLayout(
    sidebarPanel(
      
      checkboxGroupInput('factions_input', 
                         'Choose faction',
                         choices = unique(list_initiators$factions),
                         selected = unique(list_initiators$factions)),
      
      sliderInput("amends_connection",
                  "Connections",
                  min = 1, 
                  max = 15,
                  value = 5)),
    
    mainPanel(forceNetworkOutput("network_amends"),
              tableOutput("table_nodes"), 
              tableOutput("table_edges")
    )
  )
)


# server ####
server <- function(input, output, session) {
  
  # Download data
  list_initiators <- as.data.frame(list_initiators)
  edges_for_gephy <- as.data.frame(edges_for_gephy)
  
  # Nodes\vertices  
  nodes_rea <-reactive({
    
    nodes_reactive <- list_initiators%>%
      filter(factions %in% input$factions_input) 
  })
  
  # Edges\links   
  links_rea <-reactive({
    
    edges_reactive <- edges_for_gephy%>%
      filter(Value >= input$amends_connection) 
    
  })
  

# Render tables showing content of uploaded files 
output$table_edges <- renderTable({
  links_rea() # Edges
})

output$table_nodes <- renderTable({
  nodes_rea() #Nodes
})

output$network_amends <- renderForceNetwork({
  links1 <-links_rea()
  # These three lines have to solve problem with zero-indexing, but it doesn't work 
  # I still have this warning: It looks like Source/Target is not zero-indexed. This is required in JavaScript and so your plot may not render.
  links1$Source <- match(links_rea()$Source, nodes_rea()$ID_mps)-1
  links1$Target <- match(links_rea()$Target, nodes_rea()$ID_mps)-1
  
  forceNetwork(Links = links1, # source target   value
               Nodes = nodes_rea(), # name
               Source = "Source",
               Target = "Target", 
               Value = "Value",
               Group = "factions", # Colors
               NodeID = "names_mps",
               Nodesize = "weight_name",
               opacity = 1, 
               fontSize = 18, 
               zoom = T,  
               legend = TRUE,
               bounded = TRUE,
               charge=-10)
  
})


}

runApp(shinyApp(ui, server))

`list_initiators <- read.csv(...)` returns on my computer an empty dataset — Waldi, Sep 20 '20 at 20:04
@Waldi Weird. The link works properly https://raw.githubusercontent.com/Okssana/shiny_app_network/master/nodes_amends_20_09_2020.csv — Oksana, Sep 20 '20 at 20:09
probably an encoding problem : I don't see the characters in the link — Waldi, Sep 20 '20 at 20:15
fileEncoding = "Windows-1251" , It is mentioned in read.csv() as well — Oksana, Sep 20 '20 at 20:49

score 0 · Answer 1 · answered Sep 21 '20 at 13:11

After filtering the nodes data frame (nodes_rea()), your links data frame (links1/links_rea()) will have links/row where the Source and/or the Target value/s are not found in your nodes data frame, and therefore your match commands to re-index the nodes in your links data frame will result in some NA values. Filter out those rows in the links data frame that have NAs first and it should work, i.e.

links1 <- links1 %>% filter(!is.na(Source) & !is.na(Target))

Zero-index problem and filtering issue in shiny

1 Answers1