sankey plot for correctly set node height ?

[LuffyLuffy]

Hi, I found there is some code in sanekyNetwork.js to add a parameter so that we can predefined the height of a node. Previously, the node height was by accumulating in the links part. But the value is not scale according to the canvas height. don't know how to attached the files.

links file:

N1	N2	value
T_006	T_007	226
T_004	T_007	28
T_003	T_007	26
T_002	T_007	3
T_001	T_007	4
T_006_new	T_007	21
T_004_new	T_007	21
T_003_new	T_007	7
T_002_new	T_007	9
T_004	T_006	193
T_003	T_006	34
T_002	T_006	5
T_001	T_006	23
T_004_new	T_006	46
T_003_new	T_006	14
T_002_new	T_006	11
T_003	T_004	146
T_002	T_004	23
T_001	T_004	37
T_003_new	T_004	20
T_002_new	T_004	24
T_002	T_003	151
T_001	T_003	128
T_002_new	T_003	30
T_001	T_002	191

nodes:file

Id	height
T_007	345
T_006	326
T_004	250
T_003	309
T_002	191
T_001	557
T_007_new	52
T_006_new	128
T_004_new	128
T_003_new	115
T_002_new	112

R code: library(networkD3) library(htmlwidgets) library(tidyverse) options(stringsAsFactors = F) links1<-read.csv('edges_test.csv') nodes1<-read.csv('node.csv') nodeID<-rownames(nodes1) names(nodeID)<-nodes1$Id

names(links) = c("source", "target", "value")

links1$source<-as.numeric(unname(nodeID[links1$N1]))-1 links1$target<-as.numeric(unname(nodeID[links1$N2]))-1 nodes1$name<-as.numeric(unname(nodeID[nodes1$Id]))-1 nodes1$ngroup<-gsub("_new","",nodes1$Id) color_scale1<-as.data.frame(nodes1) color_scale1$range<-brewer.pal(n=nrow(color_scale1),name='Paired')[as.numeric(factor(color_scale1$ngroup))] color_scale1$domain=color_scale1$Id

sankeyNetwork(Links = links1, Nodes = nodes1,#nodePadding=100, Source = "source", Target = "target", Value = "value", LinkGroup = 'N1',NodeGroup = 'ngroup', NodeID = "Id",#height = 200, fontSize= 12, nodeWidth = 10,sinksRight = T,iterations = 0)

node.append("rect")
        **.attr("height", function(d) { return d.value; })**
        .attr("width", sankey.nodeWidth())
        .style("fill", function(d) {
            return d.color = color_node(d); })
        .style("stroke", function(d) { return d3.rgb(d.color).darker(2); })
        .style("opacity", 0.9)
        .style("cursor", "move")
        .append("title")
        .append("foreignObject")
        .append("xhtml:body")
        .html(function(d) { return "<pre>" + d.name + "<br>" + format(d.value) + 
            " " + options.units + "</pre>"; });

[LuffyLuffy]

take T_001 for example, the node has 557, it can flow to others, but the sum of its contribution to other is 383. Thus, it still keep 174. Then the node height should be 557. However, presently, sankeyNetwork only give a length of 383, and the 174 was ignored. Thus, I wonder if it is possible to give a nodeHeight setting option, so that the I can present my data correctly. Any hint on achieving my purpose would be highly appreciated!

[cjyetman]

Please make a fully reproducible example. I should be able to copy-paste your code and click run and see the same result.

[LuffyLuffy]

Please make a fully reproducible example. I should be able to copy-paste your code and click run and see the same result.

Thanks for your prompt reply! Below is a reproducible example. I hope the node height can be set.

rm(list=ls()) library(stringi) library(networkD3) library(htmlwidgets) library(tidyverse) library(RColorBrewer)

install.packages('networkD3')

rm(list=ls()) options(stringsAsFactors = F) links1<-as.data.frame(matrix(c( "T_006","T_007",226, "T_004","T_007",28, "T_003","T_007",26, "T_002","T_007",3, "T_001","T_007",4, "T_006_new","T_007",21, "T_004_new","T_007",21, "T_003_new","T_007",7, "T_002_new","T_007",9, "T_004","T_006",193, "T_003","T_006",34, "T_002","T_006",5, "T_001","T_006",23, "T_004_new","T_006",46, "T_003_new","T_006",14, "T_002_new","T_006",11, "T_003","T_004",146, "T_002","T_004",23, "T_001","T_004",37, "T_003_new","T_004",20, "T_002_new","T_004",24, "T_002","T_003",151, "T_001","T_003",128, "T_002_new","T_003",30, "T_001","T_002",191),nrow = 25,byrow = T, )) colnames(links1)<-c('N1','N2','value') nodes1<-as.data.frame(matrix( c("T_007",345, "T_006",326, "T_004",250, "T_003",309, "T_002",191, "T_001",557, "T_007_new",52, "T_006_new",128, "T_004_new",128, "T_003_new",115, "T_002_new",112),nrow = 11,byrow = T )) colnames(nodes1)<-c("Id","height") nodeID<-rownames(nodes1) names(nodeID)<-nodes1$Id

names(links) = c("source", "target", "value")

links1$source<-as.numeric(unname(nodeID[links1$N1]))-1 links1$target<-as.numeric(unname(nodeID[links1$N2]))-1 nodes1$name<-as.numeric(unname(nodeID[nodes1$Id]))-1 nodes1$ngroup<-gsub("_new","",nodes1$Id) color_scale1<-as.data.frame(nodes1) color_scale1$range<-brewer.pal(n=nrow(color_scale1),name='Paired')[as.numeric(factor(color_scale1$ngroup))] color_scale1$domain=color_scale1$Id

sankeyNetwork(Links = links1, Nodes = nodes1,#nodePadding=100, Source = "source", Target = "target", Value = "value", LinkGroup = 'N1',NodeGroup = 'ngroup', NodeID = "Id",#height = 200, fontSize= 12, nodeWidth = 10,sinksRight = T,iterations = 0)

[cjyetman]

No, sorry. Sankey plots are intended to show flows between nodes, so the node size always reflects the amount of flow out of it. You could of course write a custom D3 visualization in JavaScript to do what you want, but that's out of scope for this package/function.

[LuffyLuffy]

Yes, but it's also have some meaning to show the total source. Thanks, I'll try to learn some D3 javascript.

[cjyetman]

You could sort of force a source node to have a specific size by adding a source node before it that flows in the value that you want it to start with...

library(tidyverse)
library(networkD3)

links <- tibble::tribble(
  ~source, ~target, ~value,
  "a",     "b",    200,
  "b",     "c",     25,
  "b",     "d",     25,
  "b",     "e",     25,
  "b",     "f",     25
)

nodes <- data.frame(
  name = unique(c(as.character(links$source), as.character(links$target))))

links$IDsource <- match(links$source, nodes$name)-1
links$IDtarget <- match(links$target, nodes$name)-1

sankeyNetwork(Links = links, Nodes = nodes,
              Source = "IDsource", Target = "IDtarget",
              Value = "value", NodeID = "name", 
              sinksRight=FALSE)

[LuffyLuffy]

Exactly, I only need to calculate the left part and make a self link, and set the link color as white or just keep it ! Thanks!