Network chord diagram woes in R

Question

I have some data similar to the data.frame d as follows.

d <- structure(list(ID = c("KP1009", "GP3040", "KP1757", "GP2243", 
                           "KP682", "KP1789", "KP1933", "KP1662", "KP1718", "GP3339", "GP4007", 
                           "GP3398", "GP6720", "KP808", "KP1154", "KP748", "GP4263", "GP1132", 
                           "GP5881", "GP6291", "KP1004", "KP1998", "GP4123", "GP5930", "KP1070", 
                           "KP905", "KP579", "KP1100", "KP587", "GP913", "GP4864", "KP1513", 
                           "GP5979", "KP730", "KP1412", "KP615", "KP1315", "KP993", "GP1521", 
                           "KP1034", "KP651", "GP2876", "GP4715", "GP5056", "GP555", "GP408", 
                           "GP4217", "GP641"),
                    Type = c("B", "A", "B", "A", "B", "B", "B", 
                             "B", "B", "A", "A", "A", "A", "B", "B", "B", "A", "A", "A", "A", 
                             "B", "B", "A", "A", "B", "B", "B", "B", "B", "A", "A", "B", "A", 
                             "B", "B", "B", "B", "B", "A", "B", "B", "A", "A", "A", "A", "A", 
                             "A", "A"),
                    Set = c(15L, 1L, 10L, 21L, 5L, 9L, 12L, 15L, 16L, 
                            19L, 22L, 3L, 12L, 22L, 15L, 25L, 10L, 25L, 12L, 3L, 10L, 8L, 
                            8L, 20L, 20L, 19L, 25L, 15L, 6L, 21L, 9L, 5L, 24L, 9L, 20L, 5L, 
                            2L, 2L, 11L, 9L, 16L, 10L, 21L, 4L, 1L, 8L, 5L, 11L), Loc = c(3L, 
                                                                                          2L, 3L, 1L, 3L, 3L, 3L, 1L, 2L, 1L, 3L, 1L, 1L, 2L, 2L, 1L, 3L, 
                                                                                          2L, 2L, 2L, 3L, 2L, 3L, 2L, 1L, 3L, 3L, 3L, 2L, 3L, 1L, 3L, 3L, 
                                                                                          1L, 3L, 2L, 3L, 1L, 1L, 1L, 2L, 3L, 3L, 3L, 2L, 2L, 3L, 3L)),
               .Names = c("ID", "Type", "Set", "Loc"), class = "data.frame",
               row.names = c(NA, -48L))

I want to explore the relationships between members of d$ID using a chord diagram similar to the one below.

enter image description here

It seesms there ar several options to do so in R. (Chord diagram in R).

In my data the relationships are according to d$Set (not directional) and the grouping is according to d$Loc. The following are my attempts to map theser relationships as a chord diagram.

Attempt 1: Using `igraph`

I have tried igraph as follows with node size according to degree.

# Get vertex relationships
sets <- unique(d$Set[duplicated(d$Set)])
rel <-  vector("list", length(sets))
for (i in 1:length(sets)) {
  rel[[i]] <- as.data.frame(t(combn(subset(d, d$Set ==sets[i])$ID, 2)))
}
library(data.table)
rel <- rbindlist(rel)

# Get the graph
g <- graph.data.frame(rel, directed=F, vertices=d)
clr <- as.factor(V(g)$Loc)
levels(clr) <- c("salmon", "wheat", "lightskyblue")
V(g)$color <- as.character(clr)

# Plot
plot(g, layout = layout.circle, vertex.size=degree(g)*5, vertex.label=NA)

enter image description here

How to modify the plot to look like the first figure? It seems that there are no options to modify igraph layout.circle.

Attempt 2: Using `Circlize`

It seems smoother bezier curves and grouping are possible in the R package circlize. But here I am not able to group the nodes as well as adjust their size according to degree as they are plotted as sectors.

par(mar = c(1, 1, 1, 1), lwd = 0.1, cex = 0.7)
circos.initialize(factors = as.factor(d$ID), xlim = c(0, 10))
circos.trackPlotRegion(factors = as.factor(d$ID), ylim = c(0, 0.5), bg.col = V(g)$color,
                       bg.border = NA, track.height = 0.05)
for(i in 1:nrow(rel)) {
  circos.link(rel[i,1], 0, rel[i,2],0, h = 0.4)

}

enter image description here

Here however there are no options to modify the nodes. In fact they can be only plotted as sectors? In this case is there any way to modify the sectors into circular nodes of size according to the degree?

Attempt 3: Using `edgebundleR`(https://github.com/garthtarr/edgebundleR)

require(edgebundleR)
edgebundle(g,tension = 0.1,cutoff = 0.5, fontsize = 18,padding=40)

enter image description here It seems here there are limited options to modify the aesthetics.

You might find what you need in the `circlize` vignette [How to make Chord Diagram](http://cran.r-project.org/web/packages/circlize/vignettes/circular_visualization_of_matrix.pdf) — Henrik, Jun 08 '15 at 12:37
You can group the variables by ordering the adjacency matrix and add some curve to the edges with edge.curve argument. Apologies code dump: `m — user20650, Jun 08 '15 at 14:25
Also [qgraph](http://sachaepskamp.com/qgraph) has some nice features — user20650, Jun 08 '15 at 14:27
@user20650 Can you kindly post it as an answer. I think it is close except for the bezier curve part. — Crops, Jun 08 '15 at 14:44
Hi Crops; yup almost there, but not quite. I cant post an answer as the question has been closed as a dup (hence code dump above). — user20650, Jun 08 '15 at 14:53
@RomanLuštrik `networkD3` (http://christophergandrud.github.io/networkD3/) looks great. But currently this `R` interface supports only *Force directed networks*, *Sankey diagrams* and *Reingold-Tilford Tree graphs*. Not circular layout — Crops, Jun 08 '15 at 14:55
I understand you are using R, but why not to try circos (http://circos.ca/)? One alternative to use R + circos idea is http://www.bioconductor.org/packages/release/bioc/html/OmicCircos.html. — AndreiR, Aug 09 '15 at 23:57
I'm happy to work on adding the aesthetics to `edgeBundler`. Do you have the source code for the referenced picture? — timelyportfolio, Aug 27 '15 at 18:16
never mind I found it at http://seekshreyas.github.io/beerviz/ — timelyportfolio, Aug 27 '15 at 18:24

timelyportfolio · Accepted Answer · 2016-05-18T11:33:23.683

I made a bunch of changes to edgebundleR. These are now in the main repo. The following code should get you close to the desired result. live example

# devtools::install_github("garthtarr/edgebundleR")

library(edgebundleR)
library(igraph)
library(data.table)

d <- structure(list(ID = c("KP1009", "GP3040", "KP1757", "GP2243", 
                           "KP682", "KP1789", "KP1933", "KP1662", "KP1718", "GP3339", "GP4007", 
                           "GP3398", "GP6720", "KP808", "KP1154", "KP748", "GP4263", "GP1132", 
                           "GP5881", "GP6291", "KP1004", "KP1998", "GP4123", "GP5930", "KP1070", 
                           "KP905", "KP579", "KP1100", "KP587", "GP913", "GP4864", "KP1513", 
                           "GP5979", "KP730", "KP1412", "KP615", "KP1315", "KP993", "GP1521", 
                           "KP1034", "KP651", "GP2876", "GP4715", "GP5056", "GP555", "GP408", 
                           "GP4217", "GP641"),
                    Type = c("B", "A", "B", "A", "B", "B", "B", 
                             "B", "B", "A", "A", "A", "A", "B", "B", "B", "A", "A", "A", "A", 
                             "B", "B", "A", "A", "B", "B", "B", "B", "B", "A", "A", "B", "A", 
                             "B", "B", "B", "B", "B", "A", "B", "B", "A", "A", "A", "A", "A", 
                             "A", "A"),
                    Set = c(15L, 1L, 10L, 21L, 5L, 9L, 12L, 15L, 16L, 
                            19L, 22L, 3L, 12L, 22L, 15L, 25L, 10L, 25L, 12L, 3L, 10L, 8L, 
                            8L, 20L, 20L, 19L, 25L, 15L, 6L, 21L, 9L, 5L, 24L, 9L, 20L, 5L, 
                            2L, 2L, 11L, 9L, 16L, 10L, 21L, 4L, 1L, 8L, 5L, 11L), Loc = c(3L, 
                                                                                          2L, 3L, 1L, 3L, 3L, 3L, 1L, 2L, 1L, 3L, 1L, 1L, 2L, 2L, 1L, 3L, 
                                                                                          2L, 2L, 2L, 3L, 2L, 3L, 2L, 1L, 3L, 3L, 3L, 2L, 3L, 1L, 3L, 3L, 
                                                                                          1L, 3L, 2L, 3L, 1L, 1L, 1L, 2L, 3L, 3L, 3L, 2L, 2L, 3L, 3L)),
               .Names = c("ID", "Type", "Set", "Loc"), class = "data.frame",
               row.names = c(NA, -48L))

# let's add Loc to our ID
d$key <- d$ID
d$ID <- paste0(d$Loc,".",d$ID)

# Get vertex relationships
sets <- unique(d$Set[duplicated(d$Set)])
rel <-  vector("list", length(sets))
for (i in 1:length(sets)) {
  rel[[i]] <- as.data.frame(t(combn(subset(d, d$Set ==sets[i])$ID, 2)))
}

rel <- rbindlist(rel)

# Get the graph
g <- graph.data.frame(rel, directed=F, vertices=d)
clr <- as.factor(V(g)$Loc)
levels(clr) <- c("salmon", "wheat", "lightskyblue")
V(g)$color <- as.character(clr)
V(g)$size = degree(g)*5
# Plot
plot(g, layout = layout.circle, vertex.label=NA)


edgebundle( g )->eb

eb

this doesn't work if you want to color each edge according to some other parameter. E.g., in igraph you can color the edges via `E(g)$color` but the `edgebundleR` package is only coloring edges using the source node's color. so all outgoing edges have to be the same. — rrs, Feb 05 '16 at 19:31
I see what should have been obvious. Sorry it took me a while to understand. These lines https://github.com/garthtarr/edgebundleR/blob/master/inst/htmlwidgets/edgebundleR.js#L80 demonstrate the problem you mention. Let me play a bit and try to come up with an answer. — timelyportfolio, Feb 05 '16 at 20:00
Thanks @timelyportfolio. I've also been looking at that line of code too but I'm not sure how to get the edge properties from the graph. I'm pretty good with R, but don't know much about javascript. So I can't even figure out how the source node is even being passed in! — rrs, Feb 05 '16 at 20:28
After refamiliarizing myself with the code, I realize this will require a rewrite of much of the code or will require a hack. I'll post the hack in an answer below. — timelyportfolio, Feb 05 '16 at 20:52

score 8 · Answer 2 · answered Feb 05 '16 at 20:54

I hate to add another answer for a different problem, but I don't know of any way to handle the additional question posed in the comment. The comment asked how might we color the edges. Generally, the response would be easy, but in this case, the answer requires a rewrite of much of the code in edgebundleR or requires a hack. I'll go with the hack below.

library(edgebundleR)
library(igraph)
library(data.table)

d <- structure(list(ID = c("KP1009", "GP3040", "KP1757", "GP2243", 
                           "KP682", "KP1789", "KP1933", "KP1662", "KP1718", "GP3339", "GP4007", 
                           "GP3398", "GP6720", "KP808", "KP1154", "KP748", "GP4263", "GP1132", 
                           "GP5881", "GP6291", "KP1004", "KP1998", "GP4123", "GP5930", "KP1070", 
                           "KP905", "KP579", "KP1100", "KP587", "GP913", "GP4864", "KP1513", 
                           "GP5979", "KP730", "KP1412", "KP615", "KP1315", "KP993", "GP1521", 
                           "KP1034", "KP651", "GP2876", "GP4715", "GP5056", "GP555", "GP408", 
                           "GP4217", "GP641"),
                    Type = c("B", "A", "B", "A", "B", "B", "B", 
                             "B", "B", "A", "A", "A", "A", "B", "B", "B", "A", "A", "A", "A", 
                             "B", "B", "A", "A", "B", "B", "B", "B", "B", "A", "A", "B", "A", 
                             "B", "B", "B", "B", "B", "A", "B", "B", "A", "A", "A", "A", "A", 
                             "A", "A"),
                    Set = c(15L, 1L, 10L, 21L, 5L, 9L, 12L, 15L, 16L, 
                            19L, 22L, 3L, 12L, 22L, 15L, 25L, 10L, 25L, 12L, 3L, 10L, 8L, 
                            8L, 20L, 20L, 19L, 25L, 15L, 6L, 21L, 9L, 5L, 24L, 9L, 20L, 5L, 
                            2L, 2L, 11L, 9L, 16L, 10L, 21L, 4L, 1L, 8L, 5L, 11L), Loc = c(3L, 
                                                                                          2L, 3L, 1L, 3L, 3L, 3L, 1L, 2L, 1L, 3L, 1L, 1L, 2L, 2L, 1L, 3L, 
                                                                                          2L, 2L, 2L, 3L, 2L, 3L, 2L, 1L, 3L, 3L, 3L, 2L, 3L, 1L, 3L, 3L, 
                                                                                          1L, 3L, 2L, 3L, 1L, 1L, 1L, 2L, 3L, 3L, 3L, 2L, 2L, 3L, 3L)),
               .Names = c("ID", "Type", "Set", "Loc"), class = "data.frame",
               row.names = c(NA, -48L))

# let's add Loc to our ID
d$key <- d$ID
d$ID <- paste0(d$Loc,".",d$ID)

# Get vertex relationships
sets <- unique(d$Set[duplicated(d$Set)])
rel <-  vector("list", length(sets))
for (i in 1:length(sets)) {
  rel[[i]] <- as.data.frame(t(combn(subset(d, d$Set ==sets[i])$ID, 2)))
}

rel <- rbindlist(rel)

# Get the graph
g <- graph.data.frame(rel, directed=F, vertices=d)
clr <- as.factor(V(g)$Loc)
levels(clr) <- c("salmon", "wheat", "lightskyblue")
V(g)$color <- as.character(clr)

# Plot
plot(g, layout = layout.circle, vertex.size=degree(g)*5, vertex.label=NA)


edgebundle( g )->eb

eb

# temporary hack to accomplish edge coloring
# requires newest Github version of htmlwidgets
# devtools::install_github("ramnathv/htmlwidgets")

# add some imaginary colors
E(g)$color <- c("purple","green","black")[floor(runif(length(E(g)),1,4))]
# now append these edge attributes to our htmlwidget x
eb$x$edges <- jsonlite::toJSON(get.data.frame(g,what="edges"))

eb <- htmlwidgets::onRender(
  eb,
'
function(el,x){
  // loop through each of our edges supplied
  //  and change the color
  x.edges.map(function(edge){
    var source = edge.from.split(".")[1];
    var target = edge.to.split(".")[1];
    d3.select(el).select(".link.source-" + source + ".target-" + target)
      .style("stroke",edge.color);
  })
}
'
)
eb

For some reason this isn't working. I can update the edges and see `"color":"green"` for example in the big JSON goblty-gook, but when I run the code from `onRender` and below the graph ends up looking the same. — rrs, Feb 05 '16 at 21:49
any way to use `saveWidget` and post to a gist? did you install the newest `htmlwidgets` from Github? — timelyportfolio, Feb 05 '16 at 22:05
I just tried this also - after installing most recent `htmlwidgets` and `edgebundler`. This is the error message: `Error: 'onRender' is not an exported object from 'namespace:htmlwidgets'` — jalapic, Feb 07 '16 at 02:58
this functionality introduced here https://github.com/ramnathv/htmlwidgets/pull/172. Wonder why you are getting that error if you installed from Github. hmmmmmm.... I could add `tasks` functionality, but this should eliminate the need for this. — timelyportfolio, Feb 08 '16 at 01:11
@timelyportfolio it's mostly working. turns out you can't have spaces in your node name/ID. but the colors don't look right. it's almost as though the new colors are mixing with the original edge colors. — rrs, Feb 10 '16 at 21:26
Ok, the spaces make sense. The code is not as robust as I would like, but don't have time to rewrite at this point. Using the code provided, the color will replace the original color. However, the color might not appear right since `stroke-opacity` is set to `0.4`. You can add a line to set opacity to something else `.style("stroke-opacity",1)`. — timelyportfolio, Feb 11 '16 at 14:44
@timelyportfolio haha, I ended up figuring this out on my own (the stroke-opacity thing). Anyways, it seems to be working now and looks great. I know we aren't supposed to say thank you in the comments, but thank you. — rrs, Feb 11 '16 at 15:11

Network chord diagram woes in R

Attempt 1: Using `igraph`

Attempt 2: Using `Circlize`

Attempt 3: Using `edgebundleR`(https://github.com/garthtarr/edgebundleR)

2 Answers2

Linked

Network chord diagram woes in R

Attempt 1: Using igraph

Attempt 2: Using Circlize

Attempt 3: Using edgebundleR(https://github.com/garthtarr/edgebundleR)

2 Answers2

Linked

Attempt 1: Using `igraph`

Attempt 2: Using `Circlize`

Attempt 3: Using `edgebundleR`(https://github.com/garthtarr/edgebundleR)