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Created July 19, 2015 19:29
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K-means clustering of wine data
Raw
README.md

I wrote a blog post for packtpub describing the K-means clustering procedure. The codes I provided were written in R, I also pointed to another blog post of mine where I use python to explain this algotithm. I decided to write a D3 visualization of the clusters.

Raw
clusters.csv
Index Alcohol Malic Ash Alacalinity Magnesium Phenols Flavanoids Nonflavanoids Proanthocyanins Color Hue Dilution Proline cluster
1 1.514340767 -0.560668221 0.23139979 -1.166303174 1.908521507 0.806721729 1.031908069 -0.657707799 1.221438453 0.251008784 0.361158491 1.84272147 1.010159388 1
2 0.245596828 -0.498008556 -0.825667215 -2.483840525 0.01809398 0.567048088 0.731565283 -0.818410597 -0.543188717 -0.292496232 0.404908465 1.110317231 0.962526349 1
3 0.196325219 0.021171524 1.106213863 -0.267982252 0.088109814 0.806721729 1.212113741 -0.497005002 2.129959372 0.268262912 0.317408517 0.786369202 1.3912237 1
4 1.6867914 -0.345835084 0.486553895 -0.806974805 0.928299826 2.484437221 1.462399395 -0.979113395 1.029251335 1.182731669 -0.426341036 1.180740715 2.3280068 1
5 0.294868437 0.22705328 1.835225591 0.450674485 1.278378998 0.806721729 0.6614853 0.226157589 0.400275314 -0.318377423 0.361158491 0.448336476 -0.037767469 1
6 1.47738706 -0.515911317 0.304300963 -1.286079296 0.858283992 1.55769914 1.362285134 -0.175599406 0.662348656 0.729810822 0.404908465 0.335658901 2.232740722 1
7 1.711427204 -0.41744613 0.304300963 -1.465743481 -0.261969358 0.327374446 0.491291055 -0.497005002 0.679820212 0.082781041 0.273658544 1.363841775 1.724654973 1
8 1.304936428 -0.16680747 0.887510345 -0.567422559 1.488426501 0.487156874 0.481279629 -0.416653603 -0.595603386 -0.003489596 0.448658438 1.363841775 1.740532653 1
9 2.253414907 -0.623327885 -0.716315456 -1.645407665 -0.191953523 0.806721729 0.95181666 -0.577356401 0.679820212 0.061213382 0.536158386 0.335658901 0.94664867 1
10 1.058578381 -0.882917925 -0.351809592 -1.046527051 -0.121937689 1.094330099 1.122010905 -1.139816193 0.452689983 0.93254682 0.22990857 1.321587684 0.94664867 1
11 1.354208037 -0.15785609 -0.242457833 -0.447646437 0.368173151 1.046395371 1.29220515 -1.139816193 1.378682458 0.298457635 1.279907939 0.786369202 2.423272878 1
12 1.378843842 -0.766549976 -0.16955666 -0.806974805 -0.331985192 -0.151972837 0.401188219 -0.818410597 -0.036513589 -0.025057256 0.929908149 0.29340481 1.692899614 1
13 0.923081456 -0.542765459 0.158498617 -1.046527051 -0.752080198 0.487156874 0.731565283 -0.577356401 0.382803758 0.233754657 0.842408202 0.406082385 1.819921051 1
14 2.154871688 -0.542765459 0.085597444 -2.423952463 -0.61204853 1.286069013 1.662627919 0.547563185 2.129959372 0.147484019 1.279907939 0.166642538 1.280079943 1
15 1.699109302 -0.41744613 0.049146858 -2.244288279 0.158125648 1.605633868 1.612570788 -0.577356401 2.392032714 1.053325713 1.061158071 0.546929354 2.540767708 1
16 0.775266628 -0.471154414 1.215565622 -0.687198682 0.858283992 0.886612943 0.881736676 -0.497005002 -0.228700707 0.967055075 1.41115786 0.377912991 1.788165692 1
17 1.600566084 -0.372689226 1.288466795 0.151234178 1.418410667 0.806721729 1.111999479 -0.255950805 0.662348656 0.492566569 0.492408412 0.053964962 1.692899614 1
18 1.021624674 -0.68598755 0.923960931 0.151234178 1.068331495 1.046395371 1.37229656 0.306508988 0.225559753 0.665107844 0.754908255 -0.058712613 1.216569224 1
19 1.465069158 -0.668084789 0.413652722 -0.896806897 0.578220655 1.605633868 1.902902148 -0.336302204 0.470161539 1.570949537 1.192407992 0.29340481 2.963113987 1
20 0.78758453 0.683573695 0.705257413 -1.286079296 1.138347329 0.646939302 1.001873791 -1.541573188 0.120730416 0.018078063 0.011158701 1.053978443 0.311541483 1
21 1.304936428 -0.632279266 -0.315359006 -1.046527051 1.838505673 1.126286585 1.142033757 -0.979113395 0.889478886 0.255322316 0.57990836 1.546942835 0.105131647 1
22 -0.086986535 1.310170343 1.03331269 -0.267982252 0.158125648 0.183570261 0.381165367 -0.898761996 0.679820212 -0.240733849 0.317408517 1.279333594 0.073376288 1
23 0.873809846 -0.42639751 -0.023754315 -0.866862867 0.088109814 0.503135117 0.851702398 -0.738059198 0.173145084 -0.542681081 0.667408307 1.955399046 0.91489331 1
24 -0.185529754 -0.659133408 0.559455067 -0.507534498 -0.331985192 0.295417961 0.341119662 -0.818410597 -0.228700707 -0.486605166 0.57990836 1.43426526 0.851382592 1
25 0.615133898 -0.471154414 0.887510345 0.151234178 -0.261969358 0.375309174 0.581393891 -0.657707799 0.120730416 -0.663459973 0.711158281 1.701874501 0.311541483 1
26 0.060828293 -0.256321277 3.110996114 1.648435713 1.698474004 0.535091602 0.651473874 0.868968781 0.574990876 -0.637578782 0.754908255 0.828623293 0.263908444 1
27 0.479636972 -0.506959936 0.923960931 -1.01658302 -0.472016861 0.886612943 0.911770955 -0.175599406 -0.246172263 -0.111327893 -0.163841194 0.856792686 1.422979059 1
28 0.368775851 -0.55171684 -0.825667215 -0.747086744 -0.402001026 0.167592018 0.160913991 -0.738059198 -0.420887824 -0.477978102 0.273658544 0.222981325 1.708777293 1
29 1.070896284 -0.390591988 1.580071486 -0.028430007 0.50820482 1.046395371 0.941805234 0.065454791 0.295445977 -0.240733849 1.279907939 1.110317231 0.533828998 1
30 1.255664818 -0.587522363 -0.57051311 -1.046527051 -0.261969358 0.567048088 0.301073957 -0.818410597 0.679820212 -0.154463212 0.361158491 1.377926472 0.91489331 1
31 0.898445651 -0.748647215 1.215565622 0.899834945 0.088109814 1.126286585 1.222125167 -0.577356401 1.378682458 0.276889975 1.017408097 0.138473144 1.708777293 1
32 0.713677116 -0.605425124 -0.023754315 -0.118262099 0.438188986 0.902591186 1.16205661 -1.139816193 0.627405544 0.7945138 0.57990836 0.377912991 2.439150558 1
33 0.836856139 -0.453251652 -0.023754315 -0.687198682 0.298157317 0.199548504 0.6614853 0.467211786 0.662348656 -0.525426953 1.192407992 0.363828294 0.771994193 1
34 0.935399358 -0.721793073 1.215565622 0.001514024 2.258600679 1.046395371 0.711542431 1.110022978 -0.420887824 0.147484019 1.279907939 0.546929354 1.550000497 1
35 0.6274518 -0.480105794 1.03331269 -0.14820613 0.718252323 0.087700804 0.501302481 -0.577356401 -0.088928258 -0.370139806 0.623658333 0.363828294 1.105425466 1
36 0.590498093 -0.471154414 0.158498617 0.300954331 0.01809398 0.646939302 0.95181666 -0.818410597 0.470161539 0.018078063 0.361158491 1.208910109 0.549706678 1
37 0.344140046 -0.623327885 1.725873832 -1.196247204 0.718252323 0.487156874 0.651473874 -0.175599406 -0.403416268 -0.197598531 0.57990836 0.237066022 0.422685241 1
38 0.060828293 -0.614376505 0.668806826 -0.447646437 -0.121937689 0.247483232 0.401188219 -0.577356401 -0.263643819 -0.348572146 0.711158281 -0.143220794 1.137180826 1
39 0.085464098 -0.748647215 -0.971469561 -1.196247204 -0.121937689 0.167592018 0.611428169 -0.657707799 -0.385944712 -0.585816399 0.973658123 0.11030375 0.867260271 1
40 1.502022865 1.480246576 0.523004481 -1.884959911 1.978537342 1.126286585 1.011885217 -1.300518991 0.854535774 0.018078063 -0.295091115 1.293418291 0.041620929 1
41 0.689041312 -0.560668221 -0.206007247 -0.986638989 1.208363164 1.365960227 1.262170872 -0.175599406 1.308796233 0.462371846 -0.032591273 1.082147837 0.152764686 1
42 0.504272777 1.345975865 -0.898568388 -0.208094191 -0.682064364 0.247483232 0.651473874 -0.738059198 -0.193757594 -0.335631551 -0.207591167 0.546929354 0.91489331 1
43 1.083214186 -0.399543368 0.814609172 -1.345967358 0.088109814 1.525742654 1.532479379 -1.541573188 0.190616641 0.160424615 -0.338841089 1.335672381 1.105425466 1
44 0.294868437 1.471295195 -0.278908419 -0.59736659 0.228141483 0.551069845 0.601416743 -0.336302204 0.120730416 -0.301123296 -0.601340931 0.546929354 -0.212421946 1
45 0.060828293 -0.506959936 -0.971469561 -0.747086744 0.50820482 1.126286585 0.971839512 -0.657707799 0.767177993 -0.007803128 -0.338841089 1.039893746 0.43856292 1
46 1.489704963 1.525003479 0.267850376 -0.17815016 0.788268158 0.886612943 0.621439595 -0.497005002 -0.595603386 0.078467509 -0.382591062 1.011724352 1.057792427 1
47 1.699109302 1.122191348 -0.315359006 -1.046527051 0.158125648 1.525742654 1.142033757 -0.738059198 1.046722891 -0.068192574 0.361158491 1.166656018 1.010159388 1
48 1.107849991 -0.587522363 -0.898568388 -1.046527051 0.088109814 1.286069013 1.362285134 -1.220167592 0.959365111 0.44943125 -0.207591167 1.011724352 0.756116514 1
49 1.354208037 -0.283175419 0.122048031 -0.208094191 0.228141483 0.726830515 0.891748103 -0.336302204 1.378682458 0.492566569 0.492408412 0.194811931 0.994281709 1
50 1.1571216 -0.542765459 -0.351809592 -0.627310621 0.578220655 0.934547672 1.512456526 -0.336302204 0.854535774 1.657220175 0.711158281 0.687776323 1.629388895 1
51 0.060828293 -0.542765459 -1.190173079 -2.124512156 -0.542032695 0.678895787 1.242148019 -1.541573188 2.304674933 0.923919756 0.711158281 0.420167082 1.280079943 1
52 1.021624674 -0.614376505 0.851059758 -0.687198682 -0.402001026 0.247483232 0.961828086 -1.139816193 1.221438453 0.233754657 1.236157966 1.06806314 1.645266575 1
53 1.009306772 -0.524862698 0.194949204 -1.645407665 0.788268158 2.532371949 1.71268505 -0.336302204 0.487633095 0.859216778 0.22990857 0.913131474 1.40710138 1
54 0.94771726 -0.390591988 1.142664449 -0.717142713 1.068331495 1.126286585 0.761599562 0.226157589 0.155673528 0.535701888 0.754908255 0.448336476 1.994575527 1
55 0.910763553 -0.596473743 -0.424710765 -0.926750928 1.278378998 0.487156874 0.87172525 -1.220167592 0.050844191 0.341592953 -0.163841194 0.828623293 0.994281709 1
56 0.689041312 -0.542765459 0.340751549 0.300954331 1.138347329 1.062373614 0.751588136 -1.300518991 1.500983351 0.514134228 0.098658649 0.589183445 1.184813865 1
57 1.502022865 -0.569619601 -0.242457833 -0.956694959 1.278378998 1.44585144 0.971839512 -0.818410597 0.767177993 0.570210143 -0.076341246 0.983554959 0.708483475 1
58 0.356457949 -0.327932323 1.142664449 -0.806974805 0.158125648 1.126286585 1.202102314 -0.416653603 0.120730416 0.406295932 0.492408412 0.321574204 1.661144254 1
59 0.886127749 -0.81130688 0.486553895 -0.836918836 0.578220655 1.765416296 1.642605067 -1.38087039 0.784649549 0.751378481 -0.295091115 0.363828294 1.708777293 1
60 -0.776789065 -1.249924533 -3.668812953 -2.663504709 -0.822096033 -0.503494178 -1.460937052 -0.657707799 -2.045742545 -1.340684477 0.404908465 -1.115064881 -0.720507695 2
61 -0.826060674 -1.106702442 -0.315359006 -1.046527051 0.088109814 -0.391646479 -0.94034289 2.154591165 -2.063214101 -0.77129827 1.279907939 -1.326335335 -0.212421946 2
62 -0.444205702 -0.873966544 -1.263074252 -0.806974805 0.01809398 -0.439581207 -0.619977252 1.351077175 -1.696311422 0.298457635 0.098658649 -1.43901291 -0.94279521 3
63 0.824538237 -0.972431732 -1.627580115 -0.447646437 -0.402001026 -0.311755265 -0.239543057 -0.336302204 -1.504124305 -0.542681081 1.192407992 -0.213644279 -0.371198742 2
64 -0.776789065 -1.0798483 -0.752766042 -0.14820613 -0.892111867 1.925198724 1.071953774 -1.38087039 0.487633095 -0.262301509 1.148658018 0.363828294 -1.038061288 2
65 -1.023147112 -0.793404118 0.595905654 -0.14820613 0.298157317 -0.647298363 -0.279588762 0.708265983 -0.979977621 -0.90933129 2.154907414 -0.537592308 -1.244471124 2
66 -0.776789065 -1.008237255 0.705257413 -0.417702406 -0.121937689 0.199548504 0.621439595 0.065454791 0.854535774 -0.197598531 1.017408097 -0.43899943 -0.218773018 2
67 0.134735707 -1.187264868 -2.429493016 -1.345967358 -1.522254376 1.094330099 1.152045184 -0.818410597 1.203966897 0.1043487 0.711158281 0.800453899 -0.777667342 2
68 -0.776789065 -1.044042777 -1.627580115 0.031458055 -1.522254376 -0.295777022 -0.029303107 -0.738059198 -0.962506065 -0.163090276 0.711158281 1.222994806 -0.752263054 2
69 0.41804746 -1.249924533 -0.023754315 -0.747086744 0.718252323 0.375309174 -0.73010294 1.511779973 -2.045742545 -0.814433589 0.273658544 -0.960133215 0.009865569 2
70 -0.973875502 -1.026140016 -2.247240084 -0.806974805 3.588901532 -0.711211334 -0.750125793 -1.782627385 1.588341132 -0.952466609 1.41115786 0.645522233 -0.09175158 2
71 -0.875332284 -0.650182027 -0.57051311 0.2710103 0.228141483 -1.909579543 -1.010422874 0.065454791 -0.228700707 -0.866195971 -0.225091157 -1.115064881 0.390929881 2
72 1.058578381 -0.739695834 1.106213863 1.648435713 -0.962127701 1.046395371 0.831679545 -1.220167592 0.487633095 -0.723849419 1.76115765 0.772284505 -1.069816648 2
73 0.602815995 -0.605425124 -0.461161351 1.348995406 -0.892111867 -0.663276606 -0.189485926 -0.738059198 -0.979977621 -0.568562272 0.098658649 0.237066022 -0.87293342 2
74 -0.013079121 -0.596473743 0.851059758 3.145637249 2.74871152 1.605633868 0.861713824 -1.220167592 0.6448771 -0.736790015 1.542407782 1.2511642 0.756116514 1
75 -1.28182306 -1.115653823 -0.242457833 0.450674485 0.088109814 1.73345981 0.11085686 -1.862978784 0.10325886 -0.797179461 0.142408622 0.730030414 0.441738456 2
76 -1.65136013 -0.408494749 -1.627580115 -1.046527051 -0.191953523 -1.094689161 -0.459794433 -0.175599406 -0.770318947 -0.542681081 1.192407992 -0.66435458 -1.012657001 2
77 0.036192488 -1.285730056 -2.393042429 -1.046527051 -0.962127701 -0.551428907 0.000731172 -0.979113395 -0.228700707 -0.197598531 1.017408097 -0.185474885 -1.126976294 2
78 -1.429637888 0.4955947 -0.497611938 -0.447646437 0.858283992 -0.91892849 -0.710080088 0.547563185 -1.11975007 -1.038737246 0.011158701 -0.129136098 -0.784018414 2
79 -0.826060674 -1.20516763 -1.518228356 -1.405855419 2.538664016 -0.63132012 -0.1794745 -0.095248007 2.042601591 -0.715222356 0.448658438 -0.424914733 0.009865569 2
80 -0.370298288 1.372830007 0.122048031 1.049555099 0.088109814 0.854656458 0.521325333 0.547563185 0.627405544 -1.073245501 1.017408097 0.730030414 -0.901513243 2
81 -1.232551451 -1.267827295 -1.335975424 -0.14820613 -0.962127701 0.199548504 0.230993974 -0.497005002 -0.281115375 -1.103440224 1.848657598 0.715945717 -1.488987391 2
82 -0.345662484 -0.471154414 -0.606963697 -0.208094191 -0.962127701 -0.151972837 0.501302481 -0.818410597 0.312917534 -0.499545762 0.886158176 0.744115111 -0.104453724 2
83 -1.134008233 -1.0798483 0.523004481 1.348995406 -1.522254376 -0.471537693 -0.449783007 0.306508988 -0.333530044 -1.23284618 1.542407782 0.152557841 -0.371198742 2
84 0.060828293 1.363878627 -0.16955666 0.899834945 -1.032143536 -1.03077619 -0.439771581 1.993888367 0.050844191 -0.111327893 -0.513840984 -0.84745564 -0.736385375 3
85 -1.429637888 -1.294681437 0.778158586 -0.447646437 -0.402001026 -0.151972837 0.180936843 -1.139816193 1.326267789 -0.866195971 -0.732590852 0.65960693 -0.720507695 2
86 -0.407251995 -1.21411901 -0.461161351 -0.447646437 -0.051921855 -0.151972837 -0.089371664 -0.497005002 -0.228700707 -1.051677842 1.192407992 0.772284505 -0.94279521 2
87 -1.035465014 -0.650182027 -0.206007247 0.989667037 -0.682064364 -0.823059034 -0.339657319 0.547563185 -0.053985145 -1.125007884 1.629907729 -0.495338217 -0.799896093 2
88 -1.663678033 -0.596473743 0.923960931 1.94787602 -0.822096033 -0.599363635 -0.419748728 0.306508988 -0.43835938 -1.060304905 1.76115765 0.842707989 -0.587135186 2
89 -1.675995935 -0.247369897 0.340751549 0.630338669 -1.10215937 -0.551428907 -0.339657319 0.94932018 -0.420887824 -0.974034268 0.186158596 0.194811931 -0.212421946 2
90 -1.134008233 -0.900820687 -0.242457833 1.229219283 -2.082381051 -0.151972837 -0.439771581 0.467211786 -0.368473156 -1.431268647 0.492408412 0.842707989 -0.387076422 2
91 -1.134008233 -0.453251652 -0.16955666 -0.297926283 -1.312206873 -1.110667404 -0.529874417 1.270725776 0.085787304 -1.146575543 0.536158386 -0.48125352 -0.847529132 2
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Raw
index.html
<!DOCTYPE html>
<meta charset="utf-8">
<style>
body {
font: 10px sans-serif;
}
.axis path,
.axis line {
fill: none;
stroke: #000;
shape-rendering: crispEdges;
}
.dot {
stroke: none;
}
.tooltip{
position: absolute;
width: 130px;
height: 50px;
padding: 2px;
font: 12px sans-serif;
background: lightgreen;
border: 2px;
border-radius: 5px;
/* border-left: 1px;
border-right: 1px;*/
pointer-events: none;
}
</style>
<body>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script>
var margin = {top: 20, right: 20, bottom: 30, left: 40},
width = 960 - margin.left - margin.right,
height = 500 - margin.top - margin.bottom;
var x = d3.scale.linear()
.range([0, width]);
var y = d3.scale.linear()
.range([height, 0]);
var color = d3.scale.category20();
var xAxis = d3.svg.axis()
.scale(x)
.orient("bottom");
var yAxis = d3.svg.axis()
.scale(y)
.orient("left");
var svg = d3.select("body").append("svg")
.attr("width", width + margin.left + margin.right)
.attr("height", height + margin.top + margin.bottom)
.append("g")
.attr("transform", "translate(" + margin.left + "," + margin.top + ")");
var tooltip = d3.select("body").append("div")
.attr("class", "tooltip")
.style("opacity", 0);
d3.csv("clusters.csv", function(error, data) {
if (error) throw error;
data.forEach(function(d) {
d.Alcohol = +d.Alcohol;
d.Malic = +d.Malic;
d.cluster = d.cluster;
});
x.domain(d3.extent(data, function(d) { return d.Alcohol; })).nice();
y.domain(d3.extent(data, function(d) { return d.Malic; })).nice();
svg.append("g")
.attr("class", "x axis")
.attr("transform", "translate(0," + height + ")")
.call(xAxis)
.append("text")
.attr("class", "label")
.attr("x", width)
.attr("y", -6)
.style("text-anchor", "end")
.text("Alcohol");
svg.append("g")
.attr("class", "y axis")
.call(yAxis)
.append("text")
.attr("class", "label")
.attr("transform", "rotate(-90)")
.attr("y", 6)
.attr("dy", ".71em")
.style("text-anchor", "end")
.text("Malic")
svg.selectAll(".dot")
.data(data)
.enter().append("circle")
.attr("class", "dot")
.attr("r", 5)
.attr("cx", function(d) { return x(d.Alcohol); })
.attr("cy", function(d) { return y(d.Malic); })
.style("fill", function(d) { return color(d.cluster); })
.on("mouseover", function(d){
tooltip.transition()
.duration(200)
.style("opacity", .9);
tooltip.html("Cluster: " + d.cluster + "<br/> Alcohol: " + d.Alcohol + "<br/> Malic: " + d.Malic)
.style("left", (d3.event.pageX + 10) + "px")
.style("top", (d3.event.pageY - 20) + "px");
})
.on("mouseout", function(d){
tooltip.transition()
.duration(500)
.style("opacity",0);
});
var legend = svg.selectAll(".legend")
.data(color.domain())
.enter().append("g")
.attr("class", "legend")
.attr("transform", function(d, i) { return "translate(0," + i * 20 + ")"; });
legend.append("rect")
.attr("x", width - 18)
.attr("width", 18)
.attr("height", 18)
.style("fill", color);
legend.append("text")
.attr("x", width - 24)
.attr("y", 9)
.attr("dy", ".35em")
.style("text-anchor", "end")
.text(function(d) { return d; });
});
</script>
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