Network chord diagram woes in R

Asked 8/6, 2015 at 12:2 Answered 5/2, 2016 at 20:54

Solved r data-visualization igraph graph-visualization circos

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.

Shetrit answered 8/6, 2015 at 12:2 Comment(10)

You might find what you need in the circlize vignette How to make Chord Diagram – Reata 8/6, 2015 at 12:37

What about christophergandrud.github.io/d3Network ? – Chari 8/6, 2015 at 12:46

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 <- tcrossprod(table(d[c(1,3)])) ; grp <- d[order(d$ID), "Loc"] ; m2 <- m[order(grp), order(grp) ] ; diag(m2) <- 0 ; g <- graph.adjacency(m2, mode="undirected"); clr <- as.factor(sort(grp)); levels(clr) <- c("salmon", "wheat", "lightskyblue"); V(g)$color <- as.character(clr); par(mar=rep(0,4)); plot(g, layout = layout.circle,       vertex.size=degree(g)*5, vertex.label=NA,       edge.curved=seq(-0.5, 0.5, length = ecount(g)))

– Frenchpolish 8/6, 2015 at 14:25

Also qgraph has some nice features – Frenchpolish 8/6, 2015 at 14:27

@Frenchpolish Can you kindly post it as an answer. I think it is close except for the bezier curve part. – Shetrit 8/6, 2015 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). – Frenchpolish 8/6, 2015 at 14:53

@RomanLuštrik networkD3 (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 – Shetrit 8/6, 2015 at 14:55

I understand you are using R, but why not to try circos (circos.ca)? One alternative to use R + circos idea is bioconductor.org/packages/release/bioc/html/OmicCircos.html. – Ozenfant 9/8, 2015 at 23:57

I'm happy to work on adding the aesthetics to edgeBundler. Do you have the source code for the referenced picture? – Gambia 27/8, 2015 at 18:16

never mind I found it at seekshreyas.github.io/beerviz – Gambia 27/8, 2015 at 18:24

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

Gambia answered 27/8, 2015 at 23:21 Comment(6)

How do you change the color of the edges? – Check 5/2, 2016 at 15:38

These three lines clr <- as.factor(V(g)$Loc) levels(clr) <- c("salmon", "wheat", "lightskyblue") V(g)$color <- as.character(clr) is how colors were defined. There are other methods. For instance just doing V(g)$color <- "red" would make everything red. – Gambia 5/2, 2016 at 19:11

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. – Check 5/2, 2016 at 19:31

I see what should have been obvious. Sorry it took me a while to understand. These lines github.com/garthtarr/edgebundleR/blob/master/inst/htmlwidgets/… demonstrate the problem you mention. Let me play a bit and try to come up with an answer. – Gambia 5/2, 2016 at 20:0

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! – Check 5/2, 2016 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. – Gambia 5/2, 2016 at 20:52

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

Gambia answered 5/2, 2016 at 20:54 Comment(7)

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. – Check 5/2, 2016 at 21:49

any way to use saveWidget and post to a gist? did you install the newest htmlwidgets from Github? – Gambia 5/2, 2016 at 22:5

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' – Query 7/2, 2016 at 2:58

this functionality introduced here 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. – Gambia 8/2, 2016 at 1:11

@Gambia 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. – Check 10/2, 2016 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). – Gambia 11/2, 2016 at 14:44

@Gambia 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. – Check 11/2, 2016 at 15:11

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Attempt 1: Using igraph

Attempt 2: Using Circlize

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

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Attempt 1: Using `igraph`

Attempt 2: Using `Circlize`

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