Compute a cosine dissimilarity matrix in R [closed]

Question

I want to create heatmaps based upon cosine dissimilarity.

I'm using R and have explored several packages, but cannot find a function to generate a standard cosine dissimilarity matrix. The built-in dist() function doesn't support cosine distances, also within the package arules there is a dissimilarity() function, but it only works on binary data.

Can anybody recommend a library? Or demonstrated how to calculate cosine dissimilarity within R?

Answer 1

As @Max indicated in the comments (+1) it would be simpler to "write your own" than to spend time looking for it somewhere else. As we know, the cosine similarity between two vectors $A,B$ of length $n$ is

$$ C = \frac{ \sum \limits_{i=1}^{n}A_{i} B_{i} }{ \sqrt{\sum \limits_{i=1}^{n} A_{i}^2} \cdot \sqrt{\sum \limits_{i=1}^{n} B_{i}^2} } $$

which is straightforward to generate in R. Let X be the matrix where the rows are the values we want to compute the similarity between. Then we can compute the similarity matrix with the following R code:

cos.sim <- function(ix) 
{
    A = X[ix[1],]
    B = X[ix[2],]
    return( sum(A*B)/sqrt(sum(A^2)*sum(B^2)) )
}   
n <- nrow(X) 
cmb <- expand.grid(i=1:n, j=1:n) 
C <- matrix(apply(cmb,1,cos.sim),n,n)

Then the matrix C is the cosine similarity matrix and you can pass it to whatever heatmap function you like (the only one I'm familiar with is image()).

Answer 2

---

Many answers here are computationally inefficient, try this;

---

For cosine similarity matrix

Matrix <- as.matrix(DF)
sim <- Matrix / sqrt(rowSums(Matrix * Matrix))
sim <- sim %*% t(sim)

Convert to cosine dissimilarity matrix (distance matrix).

D_sim <- as.dist(1 - sim)

Answer 3

You can use the cosine function from the lsa package:
http://cran.r-project.org/web/packages/lsa

Answer 4

The following function might be useful when working with matrices, instead of 1-d vectors:

# input: row matrices 'ma' and 'mb' (with compatible dimensions)
# output: cosine similarity matrix

cos.sim=function(ma, mb){
  mat=tcrossprod(ma, mb)
  t1=sqrt(apply(ma, 1, crossprod))
  t2=sqrt(apply(mb, 1, crossprod))
  mat / outer(t1,t2)
}

Answer 5

Ramping up some of the previous code (from @Macro) on this issue, we can wrap this into a cleaner version in the following:

df <- data.frame(t(data.frame(c1=rnorm(100),
                              c2=rnorm(100),
                              c3=rnorm(100),
                              c4=rnorm(100),
                              c5=rnorm(100),
                              c6=rnorm(100))))

#df[df > 0] <- 1
#df[df <= 0] <- 0



apply_cosine_similarity <- function(df){
  cos.sim <- function(df, ix) 
  {
    A = df[ix[1],]
    B = df[ix[2],]
    return( sum(A*B)/sqrt(sum(A^2)*sum(B^2)) )
  }   
  n <- nrow(df) 
  cmb <- expand.grid(i=1:n, j=1:n) 
  C <- matrix(apply(cmb,1,function(cmb){ cos.sim(df, cmb) }),n,n)
  C
}
apply_cosine_similarity(df)

Hope this helps!