How to plot clusters of kmeans in R and show centroids? -


i have dataset has 6497 instance, 12 attributes, , class variable called q (quality). class values can range 3 9. data can downloaded in csv format from here

i doing k-means cluster on dataset , plot it. there seems wrong plots i'm generating because don't think representing clusters. plot i'm trying generate referred answer how create cluster plot in r?

here i'm doing

library(vegan) winequality <- read.csv("wine_nocolor.csv") express <- winequality[, c("fa", "va", "ca", "rs", "ch", "fsd", "tsd", "d", "p", "s", "a")] rownames(express) <- winequality$id str(express) #'data.frame': 6497 obs. of  11 variables kclus <- kmeans(express,centers= 3, iter.max=1000, nstart=10000) #takes bit of time wine_dist <- dist(express) cmd <- cmdscale(wine_dist) #takes bit of time groups <- levels(factor(kclus$cluster)) ordiplot(cmd, type = "n") #shows warning species scores not available cols <- c("steelblue", "darkred", "darkgreen") for(i in seq_along(groups)){     points(cmd[factor(kclus$cluster) == groups[i], ], col = cols[i], pch = 16) }  # add spider , hull ordispider(cmd, factor(kclus$cluster), label = true) ordihull(cmd, factor(kclus$cluster), lty = "dotted")

the above code produces following plot. can see, clusters aren't demonstrated in clear fashion.

enter image description here

questions

  • what dim1 , dim2?
  • how can fix this?
  • additionally, r offer way produce plot similar plot generated scikit showing clusters , centroids?

the author of code (from other question) using dimension reduction using mds (multi dimensional scaling) plot cluster.

read ?cmdscale understand.

also sources here , here.

whether want dimension reduction, , before or after clustering, choice, not sure there "to fix" in code, more decide want , plot. suggest try first reduce number of variables before clustering. 11 lot. useful?

also remember variables need normalized before applying k-means.


Comments

Post a Comment

Popular posts from this blog

javascript - AngularJS custom datepicker directive -

i make custom datepicker directive custom template. but have no idea how start building it... how include date data directive? i appreciate guide or give me advice work on more precisely. it might you! follow below steps html code sample: <label>birth date</label> <input type="text" ng-model="birthdate" date-options="dateoptions" custom-datepicker/> <hr/> <pre>birthdate = {{birthdate}}</pre> <script type="text/ng-template" id="custom-datepicker.html"> <div class="enhanced-datepicker"> <div class="proxied-field-wrap"> <input type="text" ui-date-format="yy-mm-dd" ng-model="ngmodel" ui-date="dateoptions"/> </div> <label> <button class="btn" type="button"><i class="icon-calendar"></i>
Read more

javascript - jQuery date picker - Disable dates after the selection from the first date picker -

<!doctype html> <html lang="en"> <head> <meta charset="utf-8"> <title>jquery ui datepicker - default functionality</title> <link rel="stylesheet" href="//code.jquery.com/ui/1.11.4/themes/smoothness/jquery-ui.css"> <script src="//code.jquery.com/jquery-1.10.2.js"></script> <script src="//code.jquery.com/ui/1.11.4/jquery-ui.js"></script> <link rel="stylesheet" href="/resources/demos/style.css"> <script> $(function () { $("#datepicker1").datepicker(); }); </script> <script> $(function () { $("#datepicker2").datepicker(); }); </script> </head> <body> <p>date 1: <input type="text" id="datepicker1"></p> <p>date 2: <input type="t
Read more