christophergandrud / d3network Goto Github PK
View Code? Open in Web Editor NEWTools for creating D3 JavaScript network graphs from R.
Home Page: http://christophergandrud.github.io/d3Network/
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output$networkPlot and/or #networkPlot app hard-coded labels for shiny
I know this is a newly-supported feature, and I'm very excited about it. Thanks!
After some trouble-shooting I discovered that the shiny example only works when
output$networkPlot <- renderPrint({
d3Network::d3ForceNetwork(..., parentElement = "#networkPlot")
})is used. Specifically, it appears that output list slot must be labelled networkPlot, and/or the parentElement argument must be "#networkPlot". I didn't do enough digging to identify which was the constrain, or if it was both.
This was confusing, but it works pretty well now that I've figured that out. My original inclination was to change the name of the output slot to more naturally match what I was working on, but then the graphic doesn't show in the output at all.
I can't share my example yet, but a reproducible example would be to replace the relevant sections in the shiny example
# Server section (in server.R line 20...)
shinyServer(function(input, output) {
output$somethingElseEntirely <- renderPrint({
d3ForceNetwork(Nodes = MisNodes,
Links = MisLinks,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
Group = "group", width = 400, height = 500,
opacity = input$slider, standAlone = FALSE,
parentElement = '#somethingElseEntirely')
})
})
# UI section (in ui.R, line 26...)
# Show network graph
mainPanel(
htmlOutput('somethingElseEntirely')
)Change Colour
Allow the user to change the node, text, and link colour.
CRAN release of networkD3
I currently use d3Network (which is outstanding) because i have tried and failed downloading networkD3 from Github (Windows and firewalls). Any idea when you plan on releasing networkD3 to CRAN? Excited to see in Shiny. Also need htmlwidget up there i guess.
Sorry if this is the wrong place to post.
Any interest in adding a function for bipartite networks?
There is example code here . If you're interested, I can give it a shot myself, but I'm a noob to javascript (good with R though), but happy to try.
ensure node labels are not obstructed by other nodes
I have a dense network, and when my mouse hovers over nodes, the label is sometimes obstructed by other nodes. I would love it if the text was 'on top of' all nodes.
I tried my hand at this myself in the code below. The weird thing is that the stand-alone version of the code works fine when opened as an html file. But when I give it to shiny using cat() and htmlOutput(), the next labels appear at the bottom of the screen.
<style> .link { stroke: #666; opacity: 1; stroke-width: 1.5px; } .node circle { stroke: #fff; opacity: 1; stroke-width: 1.5px; } .node:not(:hover) .nodetext { display: none; } text { font: 7px serif; opacity: 1; pointer-events: none; } </style> <script src=http://d3js.org/d3.v3.min.js></script> <script> var nodes = [ { "name" : "Bart ", "group" : 5 }, { "name" : "Lisa ", "group" : 4 }, { "name" : "Marge ", "group" : 9 }, { "name" : "Homer ", "group" : 1 }, { "name" : "Smithers ", "group" : 5 }, { "name" : "Maggie ", "group" : 5 }]; var links = [ { "source" : 0, "target" : 4, "value" : 1 }]; var width = 800 height = 800; var color = d3.scale.category20(); var force = d3.layout.force() .nodes(d3.values(nodes)) .links(links) .size([width, height]) .linkDistance(50) .charge(-120) .on("tick", tick) .start(); var svg = d3.select("#networkPlot").append("svg") .attr("width", width) .attr("height", height); var link = svg.selectAll(".link") .data(force.links()) .enter().append("line") .attr("class", "link") .style("stroke-width", function(d) { return Math.sqrt(d.value); }); //added tooltip var tooltip = d3.select("body") .append("div") .style("position", "absolute") .style("color", "black") .style("background-color", "#FEFCFF") .style("border", "solid 1 #726E6D") .style("visibility", "hidden"); //updated mouseover and mouseout, added mousemove var node = svg.selectAll(".node") .data(force.nodes()) .enter().append("g") .attr("class", "node") .style("fill", function(d) { return color(d.group); }) .style("opacity", 1) .on("mouseover", function(d) { tooltip.html(d.name) .style("visibility", "visible") .attr("cursor", "hand"); }) .on("mousemove", function(){ tooltip.style("top", (d3.event.pageY - 10)+"px") .style("left",(d3.event.pageX + 10)+"px"); }) .on("mouseout", function(){ tooltip.style("visibility", "hidden"); }) .call(force.drag); node.append("circle") .attr("r", 6) function tick() { link .attr("x1", function(d) { return d.source.x; }) .attr("y1", function(d) { return d.source.y; }) .attr("x2", function(d) { return d.target.x; }) .attr("y2", function(d) { return d.target.y; }); node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; }); } </script>Shiny support
- Find a way to integrate d3Network and Shiny.
Highlight node edges
Highlight node edges when a node is hovered over (as already done with d3Sankey).
Thanks to @justmytwopence for the suggestion.
d3Tree and d3ClusterDendro colours by data attribute
Add the ability to determine the node colours with d3Tree and d3ClusterDendro based on an attribute in the data. Thanks to math on Disqus.
Show the names of the nodes only on hover like in d3ForceNetwork
Another feature that would be helpful.
Curved Force Links
Add capabilities for curved force links.
zoom doesn't work in shiny app
I can set the zoom option in d3ForceNetwork to TRUE, but the resulting app remains in the default configuration, no-zooming.
Can't create d3ForceNetwork with own data
Hi Christopher,
Thanks for that package. I tried the examples you provided at your webpage http://christophergandrud.github.io/d3Network/ and they worked fine. However, I tried the same with my own data, but wasn't able to create the d3ForceDirected graph.
I tried this:
Links <- structure(list(source = c(1, 1, 2, 2, 2, 3), target = c(2, 4,
3, 4, 5, 1), value = c(2, 5, 1, 3, 7, 2)), .Names = c("source",
"target", "value"), row.names = c(NA, -6L), class = "data.frame")
Nodes <- structure(list(name = structure(1:5, .Label = c("A", "B", "C",
"D", "E"), class = "factor"), group = c(1, 2, 2, 3, 1)), .Names = c("name",
"group"), row.names = c(NA, -5L), class = "data.frame")
d3ForceNetwork(Links = Links, Nodes = Nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "name",
Group = "group", width = 550, height = 400,
opacity = 0.9, file = '~/Desktop/exm2.html')The created page doesn't show the graph. Do you have any suggestions?
Thanks for your help.
Text default visible
Hi,
thanks for the great package! I was wondering whether it was possible to make the node labels visible per default (and maybe customize the font). Is there a way to do this?
Best
Benedikt
Stroke width
Add ability to change the line stroke-width based on values in a column of the data frame.
Uncaught TypeError: Cannot read property 'weight' of undefined
No matter how i tweak d3ForceNetwork I keep getting the following error when opened in Chrome:
Uncaught TypeError: Cannot read property 'weight' of undefined
My R call looks like the following:
d3ForceNetwork(test1, test2,Source="source", Target="target", NodeID="id", Value="weight", file="test.html",Group="group")
And the outputtet HTML file are:
<style> .link { stroke: #666; opacity: 0.6; stroke-width: 1.5px; } .node circle { stroke: #fff; opacity: 0.6; stroke-width: 1.5px; } .node:not(:hover) .nodetext { display: none; } text { font: 7px serif; opacity: 0.6; pointer-events: none; } </style> <script src=http://d3js.org/d3.v3.min.js></script> <script> var links = [ { "source" : 30, "target" : 608, "value" : 4 }, { "source" : 305, "target" : 608, "value" : 6 }, { "source" : 305, "target" : 608, "value" : 2 }, { "source" : 30, "target" : 608, "value" : 2 }, { "source" : 216, "target" : 164, "value" : 1 }, { "source" : 362, "target" : 164, "value" : 1 }, { "source" : 303, "target" : 164, "value" : 1 }, { "source" : 103, "target" : 164, "value" : 5 }, { "source" : 216, "target" : 164, "value" : 4 }, { "source" : 7, "target" : 239, "value" : 4 }, { "source" : 459, "target" : 664, "value" : 2 }, { "source" : 210, "target" : 34, "value" : 10 }, { "source" : 210, "target" : 34, "value" : 58 }, { "source" : 65, "target" : 34, "value" : 4 }, { "source" : 122, "target" : 122, "value" : 1 }, { "source" : 449, "target" : 594, "value" : 22 }, { "source" : 449, "target" : 594, "value" : 6 }, { "source" : 659, "target" : 251, "value" : 3 }, { "source" : 696, "target" : 553, "value" : 3 }, { "source" : 161, "target" : 201, "value" : 1 }, { "source" : 161, "target" : 201, "value" : 3 }, { "source" : 291, "target" : 620, "value" : 43 }, { "source" : 291, "target" : 620, "value" : 247 }, { "source" : 288, "target" : 297, "value" : 3 }, { "source" : 700, "target" : 297, "value" : 4 }, { "source" : 601, "target" : 297, "value" : 1 }, { "source" : 80, "target" : 209, "value" : 2 }, { "source" : 61, "target" : 209, "value" : 1 }, { "source" : 80, "target" : 209, "value" : 10 }, { "source" : 525, "target" : 209, "value" : 9 }, { "source" : 525, "target" : 209, "value" : 2 }, { "source" : 66, "target" : 139, "value" : 1 }, { "source" : 10, "target" : 12, "value" : 4 }, { "source" : 376, "target" : 12, "value" : 18 }, { "source" : 19, "target" : 19, "value" : 4 }, { "source" : 296, "target" : 46, "value" : 42 }, { "source" : 563, "target" : 741, "value" : 9 }, { "source" : 563, "target" : 741, "value" : 44 }, { "source" : 188, "target" : 188, "value" : 3 }, { "source" : 292, "target" : 598, "value" : 9 }, { "source" : 292, "target" : 598, "value" : 15 }, { "source" : 13, "target" : 117, "value" : 1 }, { "source" : 225, "target" : 357, "value" : 6 }, { "source" : 447, "target" : 447, "value" : 2 }, { "source" : 174, "target" : 447, "value" : 1 }, { "source" : 192, "target" : 447, "value" : 39 }, { "source" : 192, "target" : 447, "value" : 5 }, { "source" : 450, "target" : 447, "value" : 1 }, { "source" : 513, "target" : 92, "value" : 6 }, { "source" : 513, "target" : 92, "value" : 22 }, { "source" : 256, "target" : 256, "value" : 2 }, { "source" : 608, "target" : 30, "value" : 4 }, { "source" : 156, "target" : 30, "value" : 27 }, { "source" : 608, "target" : 30, "value" : 2 }, { "source" : 156, "target" : 30, "value" : 1 }, { "source" : 3, "target" : 414, "value" : 576 }, { "source" : 3, "target" : 414, "value" : 6 }, { "source" : 717, "target" : 414, "value" : 2 }, { "source" : 66, "target" : 414, "value" : 34 }, { "source" : 121, "target" : 414, "value" : 116 }, { "source" : 136, "target" : 50, "value" : 3 }, { "source" : 218, "target" : 50, "value" : 23 }, { "source" : 525, "target" : 61, "value" : 1 }, { "source" : 525, "target" : 61, "value" : 5 }, { "source" : 209, "target" : 61, "value" : 1 }, { "source" : 264, "target" : 61, "value" : 3 }, { "source" : 733, "target" : 49, "value" : 2 }, { "source" : 591, "target" : 49, "value" : 1 }, { "source" : 591, "target" : 49, "value" : 4 }, { "source" : 80, "target" : 28, "value" : 1 }, { "source" : 551, "target" : 28, "value" : 2 }, { "source" : 240, "target" : 28, "value" : 1 }, { "source" : 270, "target" : 28, "value" : 3 }, { "source" : 581, "target" : 28, "value" : 12 }, { "source" : 524, "target" : 28, "value" : 1 }, { "source" : 240, "target" 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191, "target" : 218, "value" : 94 }, { "source" : 177, "target" : 3, "value" : 12 }, { "source" : 414, "target" : 3, "value" : 3 }, { "source" : 118, "target" : 3, "value" : 144 }, { "source" : 414, "target" : 3, "value" : 727 }, { "source" : 118, "target" : 3, "value" : 10 }, { "source" : 177, "target" : 3, "value" : 12 }, { "source" : 579, "target" : 398, "value" : 14 }, { "source" : 579, "target" : 398, "value" : 24 }, { "source" : 398, "target" : 398, "value" : 1 }, { "source" : 270, "target" : 221, "value" : 4 }, { "source" : 270, "target" : 221, "value" : 17 }, { "source" : 558, "target" : 605, "value" : 3 }, { "source" : 558, "target" : 605, "value" : 1 }, { "source" : 73, "target" : 605, "value" : 2 }, { "source" : 1, "target" : 605, "value" : 16 }, { "source" : 1, "target" : 605, "value" : 18 }, { "source" : 200, "target" : 605, "value" : 11 }, { "source" : 315, "target" : 148, "value" : 143 }, { "source" : 148, "target" : 148, "value" : 2 }, { "source" : 315, "target" : 148, 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63, "group" : 1 }, { "name" : 591, "group" : 1 }, { "name" : 58, "group" : 1 }, { "name" : 760, "group" : 1 }, { "name" : 341, "group" : 1 }, { "name" : 615, "group" : 1 }, { "name" : 348, "group" : 1 }, { "name" : 145, "group" : 1 }, { "name" : 379, "group" : 1 }, { "name" : 173, "group" : 1 }, { "name" : 494, "group" : 1 }, { "name" : 13, "group" : 1 }, { "name" : 32, "group" : 1 }, { "name" : 87, "group" : 1 }, { "name" : 107, "group" : 1 }, { "name" : 490, "group" : 1 }, { "name" : 701, "group" : 1 }, { "name" : 595, "group" : 1 }, { "name" : 666, "group" : 1 }, { "name" : 337, "group" : 1 }, { "name" : 111, "group" : 1 }, { "name" : 627, "group" : 1 }, { "name" : 42, "group" : 1 }, { "name" : 358, "group" : 1 }, { "name" : 41, "group" : 1 }, { "name" : 712, "group" : 1 }, { "name" : 38, "group" : 1 }, { "name" : 372, "group" : 1 }, { "name" : 366, "group" : 1 }, { "name" : 263, "group" : 1 }, { "name" : 512, "group" : 1 }, { "name" : 485, "group" : 1 }, { "name" : 289, "group" : 1 }, { "name" : 200, "group" : 1 }, { "name" : 516, "group" : 1 }, { "name" : 343, "group" : 1 }, { "name" : 789, "group" : 1 }, { "name" : 735, "group" : 1 }, { "name" : 10, "group" : 1 }, { "name" : 696, "group" : 1 } ] ; var width = 900 height = 600; var color = d3.scale.category20(); var force = d3.layout.force() .nodes(d3.values(nodes)) .links(links) .size([width, height]) .linkDistance(50) .charge(-120) .on("tick", tick) .start(); var svg = d3.select("body").append("svg") .attr("width", width) .attr("height", height); var link = svg.selectAll(".link") .data(force.links()) .enter().append("line") .attr("class", "link") .style("stroke-width", function(d) { return Math.sqrt(d.value); }); var node = svg.selectAll(".node") .data(force.nodes()) .enter().append("g") .attr("class", "node") .style("fill", function(d) { return color(d.group); }) .style("opacity", 0.6) .on("mouseover", mouseover) .on("mouseout", mouseout) .call(force.drag); node.append("circle") .attr("r", 6) node.append("svg:text") .attr("class", "nodetext") .attr("dx", 12) .attr("dy", ".35em") .text(function(d) { return d.name }); function tick() { link .attr("x1", function(d) { return d.source.x; }) .attr("y1", function(d) { return d.source.y; }) .attr("x2", function(d) { return d.target.x; }) .attr("y2", function(d) { return d.target.y; }); node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; }); } function mouseover() { d3.select(this).select("circle").transition() .duration(750) .attr("r", 16); d3.select(this).select("text").transition() .duration(750) .attr("x", 13) .style("stroke-width", ".5px") .style("font", "17.5px serif") .style("opacity", 1); } function mouseout() { d3.select(this).select("circle").transition() .duration(750) .attr("r", 8); } </script>Force-collapsible graphs
Include the option to create force-collapsible graphs: http://mbostock.github.io/d3/talk/20111116/force-collapsible.html
Error : <!DOCTYPE html> <meta charset="utf-8"> <body>
I tried to plot a fancy dynamical graph since yesterday but there were error as show in attached right-hand-side panel inside RStudio picture. Anything wrong?
d3data %>% d3SimpleNetwork(., width=1400, height=800)
and plot molecule and dna shapes' fancy graph but looks like a funny output even though I set the width='automatic'.
d3data %>% as.list %>% d3Tree(., width=1400, height=800)
Try to run the code not in RMarkdown mode, below codes became error but its work yesterday.
> d3data <- dfm$data %>% data.frame
- Error in eval(expr, envir, enclos) : object 'dfm' not found
> d3data$X1 <- ifelse(is.na(d3data$X1),'NA',d3data$X1)
- Error in ifelse(is.na(d3data$X1), "NA", d3data$X1) :
- object 'd3data' not found
> d3data %>% d3SimpleNetwork(., width=1400, height=800)
- Error in eval(expr, envir, enclos) : object 'd3data' not found
> d3data %>% as.list %>% d3Tree(., width=1400, height=800)
- Error in eval(expr, envir, enclos) : object 'd3data' not foundd3Network generates html in the console vice popping up a webpage
When I run the d3Network package I get the below scrolling html in the console vice a webpage with the network depicted. The sample is directly off of the d3Network package site.
-Jake
require(d3Network)
Loading required package: d3Network
Source <- c("A", "A", "A", "A", "B", "B", "C", "C", "D")
Target <- c("B", "C", "D", "J", "E", "F", "G", "H", "I")
NetworkData <- data.frame(Source, Target)
d3SimpleNetwork(NetworkData, width = 400, height = 250)
<!DOCTYPE html>
<meta charset="utf-8">
<body>
Color in Sankey
Check on StackOverflow and other searches--found people with the same issue, might be a bug?
NodeGroup in sankeyNetwork does not plot color, but Group in forceNetwork works fine.
encoding in d3Network
I would like to demonstrate the node labels with Chinese, which makes errors, and I think it's a issue of encoding. Is there any solution?
One example:
Source = c("小黑", "A", "A", "A", "B", "B", "C", "C", "D")
Target = c("大毛", "C", "D", "J", "E", "F", "G", "H", "I")
NetworkData = data.frame(Source, Target)
d3SimpleNetwork(NetworkData,
file = "test_chinese.html",
width = 400, height = 250)
bug on sankey: Twh showed in all graphs!
Hi - Thanks for these great visualisations!
The sankey diagram shows for any graphs Twh for terawatt/hours (hovering on a specific flow), probably from the original Energy demo.
Feature request: it would be good to be able to specify a unit-of-measurement when available...
Thanks Enzo
[Feature request] Nested Treemap
I would love to see something like this on d3Network
Thanks!
Allow zooming in d3SimpleNetwork
Would be good to have that feature there as well. Awesome package very useful.
parentElement in d3Sankey template
Hi - thanks for this package, tried with shiny and works well!
the parentElement parameter currently doesn't work with d3Sankey() because of following references to "chart" in templates.R:
#chart { height: 500px; }
/*<p id=\"chart\"></p>*/
zooming and panning across the network
These functions are fantastic thanks for sharing them!
How might we be able to zoom and pan around network? Looks like this might be relevant: http://stackoverflow.com/q/7871425/1036500 (but I am a total javascript-idiot)...
thanks,
Ben
Sankey diagrams
Add capabilities to create Sankey diagrams (http://bost.ocks.org/mike/sankey/).
Make sure that they work with bipartite networks. See #6. Thanks @schamberlain and @pedroj.
Work with igraph package objects
It would be nice if this package could produce charts from igraph package objects. I might start writing some conversion functions for contribution if you think its worth it...
d3.layout.treemap - how to?
Hi Christopher,
can you explain how to use d3Network to build d3.layout.treemap
More about:
http://mbostock.github.io/d3/talk/20111018/treemap.html
Thank you in advance.
Best regards
Robert
Change size of Node?
Hi,
Is it possible to change the size of each node based on a vector as a parameter?
I haven't found anything in document or stackoverflow...
Thanks.
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