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Rのネットワークコード図の問題

次のようなdata.framedに似たデータがあります。

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))

以下のようなコード図を使用して、d$IDのメンバー間の関係を調べたいと思います。

enter image description here

Rでそうするいくつかのオプションがあるようです。 （ Rのコード図 ）。

私のデータでは、関係はd$Set（方向ではありません）に従っており、グループ化はd$Locに従っています。以下は、theserの関係をコードダイアグラムとしてマップする試みです。

試行1：igraphの使用

程度に応じたノードサイズで次のようにigraphを試しました。

# 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

最初の図のようにプロットを変更する方法は？ igraphlayout.circleを変更するオプションはないようです。

試行2：Circlizeの使用

Rパッケージcirclizeでは、より滑らかなベジェ曲線とグループ化が可能です。しかし、ここでは、ノードをグループ化することはできません。また、ノードはセクターとしてプロットされるため、程度に応じてサイズを調整することもできません。

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

ただし、ここではノードを変更するオプションはありません。実際、それらはセクターとしてのみプロットできますか？この場合、セクターを次数に応じたサイズの円形ノードに変更する方法はありますか？

試行3：edgebundleRの使用（ https://github.com/garthtarr/edgebundleR ）

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

enter image description here ここでは、美学を修正するための限られたオプションがあるようです。

rdata-visualizationigraphgraph-visualizationcircos
46
Crops

edgebundleRに多くの変更を加えました。これらは現在メインリポジトリにあります。次のコードを使用すると、目的の結果に近づくことができます。 実例

# 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

enter image description here

24
timelyportfolio

別の問題に別の答えを追加するのは嫌いですが、コメントにある追加の質問を処理する方法がわかりません。コメントは、どのようにエッジに色を付けるか尋ねました。一般に、応答は簡単ですが、この場合、答えにはedgebundleRの多くのコードを書き直すか、ハックが必要です。以下のハックに行きます。

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
6
timelyportfolio