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R + d3.js Parallel Coordinates of partykit
Raw
Readme.md

Introduction

This d3.js parallel coordinates plot is another experiment in how we might use interactive plots in Javascript to represent a partykit / rpart object from R. The example builds on this d3.js collapsible tree plot. Eventually, it would be nice to combine the tree and parallel coordinates into a layout with synced interactivity.

### Almost No [`rCharts`](http://rcharts.io) Also, this is fairly different from most of my interactive plots from R in that it almost completely avoids [`rCharts`](http://rcharts.io) (almost because I did use its `publish` to make this gist). I chose to exclude `rCharts` for two reasons:
  1. demo how we can use htmltools to build html/js in R
  2. help users understand some of the things rCharts does for us, such as dependency management, rendering, sharing, multi-format publishing, etc.
### Reproduce I would love for others to reproduce, fork, and improve this.

code

live example

### Thanks

It is impossible to make this list complete, but I would like to thank

Raw
code.R
library(htmltools)
library(partykit)
library(rpart)
library(pipeR)
library(rlist)
library(whisker)
#key is to define how to handle the data
#for the parallel coordinates
#expect the data = list ( partykit object, original data )
rpart_Parcoords <- function( pk = NULL, data = NULL ){
# transform our data in the way we would like
# to send it to JSON and plug into our template
# since this will be parallel coordinates
# data should be in the records form (jsonlite default)
# 1) combine the fitted data from partykit with the original data
# which allow us to see which groups each row belongs
# we'll try to be smart and sort column order by the order of splits
colorder = rapply(pk,unclass,how="unlist") %>>% #unclass and unlist the partykit
list.match("varid") %>>% #get all varids
unique %>>% unlist %>>% #squash into a vector
( names(attr(pk$terms,"dataClasses"))[c(1,.)] ) %>>% #match them with column names
( unique( c(.,colnames(data) ) ) ) #get other column names from data
# get the column name of the varids from above
data = jsonlite::toJSON( cbind( pk$fitted, data[colorder] ) )
t <- tagList(
tags$div( id = "par_container", class = "parcoords", style = "height:400px;width:100%;" )
,tags$script(
#whisker.render( readLines("./layouts/chart_parcoords.html") ) %>>% HTML
whisker.render( readLines("http://timelyportfolio.github.io/rCharts_rpart/layouts/chart_parcoords.html") ) %>>% HTML
)
) %>>%
attachDependencies(list(
htmlDependency(
name="d3"
,version="3.0"
,src=c("href"="http://d3js.org/")
,script="d3.v3.js"
)
,htmlDependency(
name="pc"
,version="0.4.0"
,src=c("href"="http://syntagmatic.github.com/parallel-coordinates/")
,script="d3.parcoords.js"
,stylesheet="d3.parcoords.css"
)
))
return(t)
}
#set up a little rpart as an example
rp <- rpart(
hp ~ cyl + disp + mpg + drat + wt + qsec + vs + am + gear + carb,
method = "anova",
data = mtcars,
control = rpart.control(minsplit = 4)
)
str(rp)
rpk <- as.party(rp)
#now make it a parallel coordinates
#with our rpart_Parcoords function
rpart_Parcoords( rpk, mtcars ) %>>% html_print() -> fpath
#rCharts:::publish_.gist(fpath,description="R + d3.js Parallel Coordinates of partykit",id=NULL)
Raw
index.html
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8"/>
<script src="http://d3js.org/d3.v3.js"></script>
<link href="http://syntagmatic.github.com/parallel-coordinates/d3.parcoords.css" rel="stylesheet" />
<script src="http://syntagmatic.github.com/parallel-coordinates/d3.parcoords.js"></script>
</head>
<body>
<div id="par_container" class="parcoords" style="height:400px;width:100%;"></div>
<script> var data = [{"$row":"Mazda RX4","(fitted)":7,"(response)":110,"hp":110,"cyl":6,"mpg":21,"disp":160,"drat":3.9,"wt":2.62,"qsec":16.46,"am":1,"carb":4,"gear":4,"vs":0},{"$row":"Mazda RX4 Wag","(fitted)":7,"(response)":110,"hp":110,"cyl":6,"mpg":21,"disp":160,"drat":3.9,"wt":2.875,"qsec":17.02,"am":1,"carb":4,"gear":4,"vs":0},{"$row":"Datsun 710","(fitted)":5,"(response)":93,"hp":93,"cyl":4,"mpg":22.8,"disp":108,"drat":3.85,"wt":2.32,"qsec":18.61,"am":1,"carb":1,"gear":4,"vs":1},{"$row":"Hornet 4 Drive","(fitted)":7,"(response)":110,"hp":110,"cyl":6,"mpg":21.4,"disp":258,"drat":3.08,"wt":3.215,"qsec":19.44,"am":0,"carb":1,"gear":3,"vs":1},{"$row":"Hornet Sportabout","(fitted)":11,"(response)":175,"hp":175,"cyl":8,"mpg":18.7,"disp":360,"drat":3.15,"wt":3.44,"qsec":17.02,"am":0,"carb":2,"gear":3,"vs":0},{"$row":"Valiant","(fitted)":7,"(response)":105,"hp":105,"cyl":6,"mpg":18.1,"disp":225,"drat":2.76,"wt":3.46,"qsec":20.22,"am":0,"carb":1,"gear":3,"vs":1},{"$row":"Duster 360","(fitted)":14,"(response)":245,"hp":245,"cyl":8,"mpg":14.3,"disp":360,"drat":3.21,"wt":3.57,"qsec":15.84,"am":0,"carb":4,"gear":3,"vs":0},{"$row":"Merc 240D","(fitted)":5,"(response)":62,"hp":62,"cyl":4,"mpg":24.4,"disp":146.7,"drat":3.69,"wt":3.19,"qsec":20,"am":0,"carb":2,"gear":4,"vs":1},{"$row":"Merc 230","(fitted)":5,"(response)":95,"hp":95,"cyl":4,"mpg":22.8,"disp":140.8,"drat":3.92,"wt":3.15,"qsec":22.9,"am":0,"carb":2,"gear":4,"vs":1},{"$row":"Merc 280","(fitted)":7,"(response)":123,"hp":123,"cyl":6,"mpg":19.2,"disp":167.6,"drat":3.92,"wt":3.44,"qsec":18.3,"am":0,"carb":4,"gear":4,"vs":1},{"$row":"Merc 280C","(fitted)":7,"(response)":123,"hp":123,"cyl":6,"mpg":17.8,"disp":167.6,"drat":3.92,"wt":3.44,"qsec":18.9,"am":0,"carb":4,"gear":4,"vs":1},{"$row":"Merc 450SE","(fitted)":11,"(response)":180,"hp":180,"cyl":8,"mpg":16.4,"disp":275.8,"drat":3.07,"wt":4.07,"qsec":17.4,"am":0,"carb":3,"gear":3,"vs":0},{"$row":"Merc 450SL","(fitted)":11,"(response)":180,"hp":180,"cyl":8,"mpg":17.3,"disp":275.8,"drat":3.07,"wt":3.73,"qsec":17.6,"am":0,"carb":3,"gear":3,"vs":0},{"$row":"Merc 450SLC","(fitted)":11,"(response)":180,"hp":180,"cyl":8,"mpg":15.2,"disp":275.8,"drat":3.07,"wt":3.78,"qsec":18,"am":0,"carb":3,"gear":3,"vs":0},{"$row":"Cadillac Fleetwood","(fitted)":12,"(response)":205,"hp":205,"cyl":8,"mpg":10.4,"disp":472,"drat":2.93,"wt":5.25,"qsec":17.98,"am":0,"carb":4,"gear":3,"vs":0},{"$row":"Lincoln Continental","(fitted)":12,"(response)":215,"hp":215,"cyl":8,"mpg":10.4,"disp":460,"drat":3,"wt":5.424,"qsec":17.82,"am":0,"carb":4,"gear":3,"vs":0},{"$row":"Chrysler Imperial","(fitted)":14,"(response)":230,"hp":230,"cyl":8,"mpg":14.7,"disp":440,"drat":3.23,"wt":5.345,"qsec":17.42,"am":0,"carb":4,"gear":3,"vs":0},{"$row":"Fiat 128","(fitted)":4,"(response)":66,"hp":66,"cyl":4,"mpg":32.4,"disp":78.7,"drat":4.08,"wt":2.2,"qsec":19.47,"am":1,"carb":1,"gear":4,"vs":1},{"$row":"Honda Civic","(fitted)":4,"(response)":52,"hp":52,"cyl":4,"mpg":30.4,"disp":75.7,"drat":4.93,"wt":1.615,"qsec":18.52,"am":1,"carb":2,"gear":4,"vs":1},{"$row":"Toyota Corolla","(fitted)":4,"(response)":65,"hp":65,"cyl":4,"mpg":33.9,"disp":71.1,"drat":4.22,"wt":1.835,"qsec":19.9,"am":1,"carb":1,"gear":4,"vs":1},{"$row":"Toyota Corona","(fitted)":5,"(response)":97,"hp":97,"cyl":4,"mpg":21.5,"disp":120.1,"drat":3.7,"wt":2.465,"qsec":20.01,"am":0,"carb":1,"gear":3,"vs":1},{"$row":"Dodge Challenger","(fitted)":11,"(response)":150,"hp":150,"cyl":8,"mpg":15.5,"disp":318,"drat":2.76,"wt":3.52,"qsec":16.87,"am":0,"carb":2,"gear":3,"vs":0},{"$row":"AMC Javelin","(fitted)":11,"(response)":150,"hp":150,"cyl":8,"mpg":15.2,"disp":304,"drat":3.15,"wt":3.435,"qsec":17.3,"am":0,"carb":2,"gear":3,"vs":0},{"$row":"Camaro Z28","(fitted)":14,"(response)":245,"hp":245,"cyl":8,"mpg":13.3,"disp":350,"drat":3.73,"wt":3.84,"qsec":15.41,"am":0,"carb":4,"gear":3,"vs":0},{"$row":"Pontiac Firebird","(fitted)":11,"(response)":175,"hp":175,"cyl":8,"mpg":19.2,"disp":400,"drat":3.08,"wt":3.845,"qsec":17.05,"am":0,"carb":2,"gear":3,"vs":0},{"$row":"Fiat X1-9","(fitted)":4,"(response)":66,"hp":66,"cyl":4,"mpg":27.3,"disp":79,"drat":4.08,"wt":1.935,"qsec":18.9,"am":1,"carb":1,"gear":4,"vs":1},{"$row":"Porsche 914-2","(fitted)":5,"(response)":91,"hp":91,"cyl":4,"mpg":26,"disp":120.3,"drat":4.43,"wt":2.14,"qsec":16.7,"am":1,"carb":2,"gear":5,"vs":0},{"$row":"Lotus Europa","(fitted)":5,"(response)":113,"hp":113,"cyl":4,"mpg":30.4,"disp":95.1,"drat":3.77,"wt":1.513,"qsec":16.9,"am":1,"carb":2,"gear":5,"vs":1},{"$row":"Ford Pantera L","(fitted)":14,"(response)":264,"hp":264,"cyl":8,"mpg":15.8,"disp":351,"drat":4.22,"wt":3.17,"qsec":14.5,"am":1,"carb":4,"gear":5,"vs":0},{"$row":"Ferrari Dino","(fitted)":8,"(response)":175,"hp":175,"cyl":6,"mpg":19.7,"disp":145,"drat":3.62,"wt":2.77,"qsec":15.5,"am":1,"carb":6,"gear":5,"vs":0},{"$row":"Maserati Bora","(fitted)":15,"(response)":335,"hp":335,"cyl":8,"mpg":15,"disp":301,"drat":3.54,"wt":3.57,"qsec":14.6,"am":1,"carb":8,"gear":5,"vs":0},{"$row":"Volvo 142E","(fitted)":7,"(response)":109,"hp":109,"cyl":4,"mpg":21.4,"disp":121,"drat":4.11,"wt":2.78,"qsec":18.6,"am":1,"carb":2,"gear":4,"vs":1}]
//sort our data by fitted or the assigned group
data = data.sort(function(a,b){
return d3.ascending(a["(fitted)"],b["(fitted)"])
});
var colorgen = d3.scale.category10();
var colors = {};
data.map(function(d,i){
colors[d["(fitted)"]] = colorgen(d["(fitted)"])
});
var color = function(d) { return colors[d["(fitted)"]]; };
var parcoords = d3.parcoords()("#par_container")
.color(color)
.alpha(0.4)
.data(data)
//.bundlingStrength(0.8) // set bundling strength
//.smoothness(0.15)
//.bundleDimension("rtn_rank")
.showControlPoints(false)
.margin({ top: 100, left: 150, bottom: 12, right: 20 })
.render()
.brushMode("1D-axes") // enable brushing
.reorderable()
.interactive() // command line mode
//remove rownames (first) label for axis
d3.select(".dimension .axis > text").remove();
//highlight paths on hover of rownames / label
d3.selectAll("#par_container > svg > g > g:nth-child(1) > g.axis > g > text")
.on("mouseover", highlight )
.on("mouseout", unhighlight )
.style("fill",function(d){
return colors[d];
})
function highlight(e){
var that = this;
var tohighlight = data.filter(function(row){
return row["$row"] == d3.select(that).datum();
});
parcoords.highlight(
tohighlight
);
}
function unhighlight(e){
var that = this;
parcoords.unhighlight(
data.filter(function(row){
return row["$row"] == d3.select(that).datum();
})
);
}</script>
</body>
</html>
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