I've been trying to put together a network / chord diagram in a similar fashion to this post: Network chord diagram woes in R
I want to expand on the solution given by @timelyportfolio as a solution to the previous question and my code is not dissimilar from that used below, however, what I would like to do is weight (I don't mean weight as an attribute, I don't want to change the thickness, just the colour depth) the edges based on a colour spectrum defined within the relationships matrix (g). The weights are based on a scale of 1-5 depending on the relationship level.
The colours would be defined by an RColorBrewer palette, ie. col.blue <- brewer.pal(5, "Blues") and i'll replace my colour levels for the 'Sets' in the below code with the 5th level of the colour spectrum for each edge group.
I've spent the last 24 hours trying to work out how to do this in R, which is relatively simple in iGraph but I lose the weighted lines as soon as I apply edgebundleR. I'm assuming it requires some kind of hack to edgebundleR, but I know nothing about Java. Anyone able to help?
@roastbeeef
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
