Question: plotting problem with loop in R
0
gravatar for smyiz
8 months ago by
smyiz20
smyiz20 wrote:

I am trying to calculate the correlation coefficient and prepare distance matrix and draw a plot of clustering. I am stuck in plotting. Here is my script:

   coef <- function(x,y){
   a <- sum(x * y) / sqrt(sum(x)^2 * sum(y)^2)
   return(a)
   }

   distance <- function(X) {
        n <- ncol(X)
        n <- nrow(X)
        distMat  <- matrix(0, nrow = n, ncol = n)

        for ( i in 1:(n-1) ) {
           for ( j in (i+1):n ) {
              v1 <- X[ , i]
              v2 <- X[ , j]
              d <- 1 - coef(v1, v2)
              distMat[i, j] <- d
              distMat[j, i] <- d
           }
        }

       for ( i in 1:n ) { distMat[i, i] <- 1 }

       hr <- hclust(distMat, method="average")  
       plot <- plot(hr)

       return(plot)
   }
plot R • 392 views
ADD COMMENTlink written 8 months ago by smyiz20
1

See this https://stackoverflow.com/questions/26034177/r-saving-multiple-ggplots-using-a-for-loop

You need to use print

ADD REPLYlink written 8 months ago by lakhujanivijay4.8k

what is exactly the problem? are you getting an error? no plot is generated?

ADD REPLYlink written 8 months ago by H.Hasani850

I call "dev.off()" and the output reads "null device". the plot is not generated :(

ADD REPLYlink modified 8 months ago • written 8 months ago by smyiz20
1

the function returns the plot, to have it save probably you need to

pdf("myPlots.pdf")
print(distance(args.....))
dev.off()
ADD REPLYlink modified 8 months ago • written 8 months ago by H.Hasani850

Thanks for your reply but I am getting this error: Error in X[, i] : object of type 'closure' is not subsettable

ADD REPLYlink written 8 months ago by smyiz20
1

the error refers to this line

v1 <- X[ , i]

can you tell the outcome of the following:

ncol(X)
nrow(X)
n

by the way, in R you can easly use function cor on a full matrix instead of looping, see Correlation matrix ...

ADD REPLYlink modified 8 months ago • written 8 months ago by H.Hasani850

ncol(X) [1] 18 nrow(X) [1] 3173 n [1] 3173

ADD REPLYlink written 8 months ago by smyiz20

"cor" function wants only these methods: "pearson", "kendall", "spearman", I wanna use uncentered-pearson

ADD REPLYlink written 8 months ago by smyiz20
1

I see, then just use a second variable to get it running. The error is due to using the same variable to loop over the columns and rows leading to going beyond X's dimensions, i.e. by setting up the same value for both loops, X has only 18 columns yet n = 3173 = nrow(X).

ADD REPLYlink modified 8 months ago • written 8 months ago by H.Hasani850

Thanks, but I didn't quite get it. Do you mean I need to change v1 <- X[ , i] to v1 <- distMat[ ,i]

ADD REPLYlink written 8 months ago by smyiz20

You should be able to compute that using matrix / vector operations without the loops. Let M <- t(X) %*% X, Let z <- diag(M). Then your uncentred cors should be M / sqrt(z %*% t(z)). !!Written but not tested!!

ADD REPLYlink written 8 months ago by russhh5.1k

What does %*% do please?

ADD REPLYlink modified 8 months ago • written 8 months ago by H.Hasani850

You could experiment or search: https://www.statmethods.net/advstats/matrix.html

ADD REPLYlink written 8 months ago by russhh5.1k

I think, your formulas equal ( x * y) / sqrt(sum(x)^2 * sum(y)^2. In uncentered correlation, it should be started with sum(x*y)

ADD REPLYlink written 8 months ago by smyiz20
1

I wrote the equation to work with all pairs of columns in one go. The [i, j] entry of t(X) %*% X is equal to sum(x[, i] * x[, j])

ADD REPLYlink written 8 months ago by russhh5.1k

Could you split up your distance computation from your plotting step, so that you can debug why R thinks your X is a function/closure?

ADD REPLYlink written 8 months ago by russhh5.1k
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