R/distances.R

In pRoloc: A unifying bioinformatics framework for spatial proteomics

setMethod("nndist", c("matrix", "matrix"), 
          function(object, query, k = 3, ...)
          nndistx_matrix(object, query, k, ...))

setMethod("nndist", c("matrix", "missing"), 
          function(object, query, k = 3,
                   dist = c("euclidean", "mahalanobis"), ...)
          nndist_matrix(object, k, match.arg(dist), ...))

setMethod("nndist", c("MSnSet", "missing"), 
          function(object, query, k = 3,
                   dist = c("euclidean", "mahalanobis"), ...)
          nndist_msnset(object, k, match.arg(dist), ...))

.mahalanobis <- function(X, y, S = cov(X)) mahalanobis(X, y, S)

.make_ans <- function(object, k) {
    ans <- matrix(NA, nrow = nrow(object), ncol = k * 2)
    rownames(ans) <- rownames(object)
    colnames(ans) <- paste0(rep(c("index", "dist"), k),
                            rep(1:k, each = 2))
    ans
}

nndist_matrix <- function(object, k, dist = dist, ...) {
    ans <- .make_ans(object, k)
    m <- seq(1, k * 2, 2)
    if (dist == "euclidean") {
        res <- get.knn(object, k = k, ...) # n by k matrix
        ans[, m] <- res$nn.index
        ans[, m + 1] <- res$nn.dist
        colnames(ans) <- paste0(colnames(ans), "euc")
    } else { ## mahalanobis   
        S <- cov(object)
        res <- apply(object, 1, ## n by n distance matrix
                     function(x) .mahalanobis(object, x, S))
        diag(res) <- Inf 
        idx <- apply(res, 2, order)
        ans[, m] <- t(idx[1:k, ])
        ans[, m + 1] <- matrix(res[idx[1:k, ]], nrow = nrow(object), ncol = k)
        colnames(ans) <- paste0(colnames(ans), "mah")
    }
    return(ans)
}

## Use of 'get.knnx' instead of 'get.knn' allows one to have a query matrix
nndistx_matrix <- function(object, query, k, ...) {
    ans <- .make_ans(query, k)
    m <- seq(1, k * 2, 2)
    res <- get.knnx(object, query, k = k, ...) # n by k matrix
    ans[, m] <- res$nn.index
    ans[, m + 1] <- res$nn.dist
    colnames(ans) <- paste0(colnames(ans), "euc")
    return(ans)
}


nndist_msnset <- function(object, k, dist = dist, ...) {
    res <- nndist_matrix(exprs(object), k, dist, ...)                  
    fData(object) <- cbind(fData(object),
                           res)
    if (validObject(object))
        return(object)
}