CODEWITHSUNDEEP
rdistancehclust
takeITeasy
takeITeasy

Reputation: 360

define data.frame as a distance and perform hierarchical clustering in R

ggg <- data.frame(row.names=c("a","b","c","d","e"),var1=c("0","0","0","0","0"),var2=c("1","1","1","1","2"))

ggg_dist <- as.matrix(ggg) %>% as.dist(.)

In as.dist.default(.) : non-square matrix

class(ggg_dist)
[1] "dist"

ggg_dist
Warning message:
In df[row(df) > col(df)] <- x :
  number of items to replace is not a multiple of replacement length

 h_ggg <- hclust(ggg_dist,method="average")

Fehler in hclust(ggg_dist, method = "average") : 
  'D' must have length (N \choose 2).

I want to perform hierarchical clustering with ggg. ggg_dist is a distance as confirmed with class() made out of ggg . I want to do hierarchical clustering with ggg_dist but this does not work. It shows above error. How can I solve that.

I tried that How to convert data.frame into distance matrix for hierarchical clustering? , but get the same error when I try to call ggg_dist.

Upvotes: 0

Views: 1207

Answers (2)

Francesco Grossetti
Francesco Grossetti

Reputation: 1595

as.dist() requires a square matrix or data.frame. Your original object ggg has 5 rows but just 2 columns.

Something like the following would work.

ggg <- data.frame(row.names = c("a", "b"), 
                  var1 = c("0", "0"), 
                  var2 = c("1", "1"))

ggg_dist <- as.dist(ggg)

h_ggg <- hclust(ggg_dist, method="average")
h_ggg
#> 
#> Call:
#> hclust(d = ggg_dist, method = "average")
#> 
#> Cluster method   : average 
#> Number of objects: 2

Created on 2020-05-27 by the reprex package (v0.3.0)

Upvotes: 0

Chris Ruehlemann
Chris Ruehlemann

Reputation: 21400

You can use the function dist:

ggg_dist <- dist(ggg, method = "euclidian")

Result:

ggg_dist
  a b c d
b 0      
c 0 0    
d 0 0 0  
e 1 1 1 1

Upvotes: 1

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