Collapsible network plot in R

Question

I am trying to implement collapsible network in R based on the blog post more network layouts. However, I am always getting the error of Object not found.

devtools::install_github
devtools::install_github("timelyportfolio/networkD3@feature/d3.chart.layout")
library(htmltools)
library(networkD3)

hc = hclust(dist(mtcars))

treeNetwork( 
   as.treeNetwork(hc, "mtcars")
)

tagList(
  lapply(
    c("tree.cartesian"
      ,"tree.radial"
      ,"cluster.cartesian"
      ,"cluster.radial"
     )
    ,function(chartType){
      hierNetwork(as.treeNetwork(hc), type=chartType, zoomable=T,    collapsible=T)
    }
  )
)
tree.cartesian

EDIT 1

How can we use these graphs for an edges file to build a network? Example:

From   To
 A      B
 A      C
 A      D
 D      L
 L      J
 J      T
 B      O

I meant to ask after which line on the code you are getting the error. — Marcelo, Mar 07 '17 at 06:17
Can you try this command: `hierNetwork( as.treeNetwork(hc), type = "tree.cartesian", zoomable = T, collapsible = T )` It should open the browser with the network chart. — Marcelo, Mar 07 '17 at 06:20
- The code should show all the types of charts but it is not working for me also. You can manually see the other types by replacing `type = "tree.cartesian"` with the other types: "tree.radial", "cluster.cartesian" and "cluster.radial" — Marcelo, Mar 07 '17 at 06:26
Yes..that should solve the issue...One more thing...is it possible to use this for a data frame which is essentially an edges file. example in the edit of the question. — NinjaR, Mar 07 '17 at 06:33

score 2 · Answer 1 · answered Sep 06 '17 at 14:34

The current official dev version of networkD3 (v0.4.9000 as of 2017.09.02) has a new function treeNetwork that enables collapsible trees.

devtools::install_github("christophergandrud/networkD3")
library(networkD3)

hc <- hclust(dist(mtcars))
treeNetwork(hc)

edges <- read.table(header = T, text = "
From   To
NA     A
A      B
A      C
A      D
D      L
L      J
J      T
B      O
")

edges <- as_treenetdf(edges, cols = c(nodeId = "To", parentId = "From"))
treeNetwork(edges)

It's still in development, so we'd appreciate feedback.

Thank you, how can we plot a vertical tree? Any plans for a new CRAN release? — GitHunter0, May 24 '22 at 02:09

score 0 · Answer 2 · answered Mar 07 '17 at 06:55

0

Yes:

library(networkD3)
to <- c("a","a","a","d","l","j","b") 
from <- c("b","c","d","l","j","t","o")
df <-data.frame(to,from)
simpleNetwork(df)

You should use the official networkD3 package:

install.packages("networkD3")

answered Mar 07 '17 at 06:55

Marcelo

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score 0 · Answer 3 · answered Mar 07 '17 at 10:03

I'm not sure what the tree.cartesian object is supposed to be in your code, but you're getting the error "Object not found" because the tree.cartesian object is never being created in your code.

Having said that, your code will work if you remove your lapply command from the tagList function. Or more succinctly...

devtools::install_github("timelyportfolio/networkD3@feature/d3.chart.layout")
library(networkD3)

hc = hclust(dist(mtcars))

hierNetwork(as.treeNetwork(hc), type = 'tree.cartesian', zoomable = T, collapsible = T)
# or
hierNetwork(as.treeNetwork(hc), type = 'tree.radial', zoomable = T, collapsible = T)
# or
hierNetwork(as.treeNetwork(hc), type = 'cluster.cartesian', zoomable = T, collapsible = T)
# or
hierNetwork(as.treeNetwork(hc), type = 'cluster.radial', zoomable = T, collapsible = T)

Just to be clear, you are using a branch of networkD3, which (as far as I know) is no longer being developed. There is some current intention to add this feature to the official networkD3 branch, but at the moment (v0.3.1), this feature (collapsible branches) is not currently available.

does this answer your question? – CJ Yetman Mar 09 '17 at 10:34 — CJ Yetman, Mar 09 '17 at 10:34

Collapsible network plot in R

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