R中的网络和弦图出现问题 [英] Network chord diagram woes in R
问题描述
我有一些类似于 data.frame d 的数据，如下所示。
d<-结构（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）），
类型= 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），类= data.frame，
row.names = c（NA，-48L））
我想使用类似于下图的和弦图来探索 d $ ID 的成员之间的关系。
在 R 中似乎有多种选择。 （）
require（edgebundleR）
edgebundle（g，张力= 0.1，截止= 0.5，字体大小= 18，填充= 40）
我做了一大堆 edgebundleR 的更改。这些现在在主仓库中。以下代码将使您接近所需的结果。
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$ID using a chord diagram similar to the one below.
It seesms there ar several options to do so in R. (Chord diagram in R).
In my data the relationships are according to d$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)$color <- as.character(clr)
# Plot
plot(g, layout = layout.circle, vertex.size=degree(g)*5, vertex.label=NA)
How to modify the plot to look like the first figure? It seems that there are no options to modify igraph layout.circle.
Attempt 2: Using Circlize
It seems smoother bezier curves and grouping are possible in the R package circlize. But here I am not able to group the nodes as well as adjust their size according to degree as they are plotted as sectors.
par(mar = c(1, 1, 1, 1), lwd = 0.1, cex = 0.7)
circos.initialize(factors = as.factor(d$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)
}
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)
It seems here there are limited options to modify the aesthetics.
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
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