allow compute landmarks to be used without Background

R/cluster.R

@@ -8,25 +8,31 @@ select_top <-function(x, n_top){
 #' compute landmarks
 #' @name computeLandmarks
 #' @param ForeGround matrix or data frame of Foreground values
-#' @param BackGround matrix or data frame of BackGround values
+#' @param BackGround matrix or data frame of BackGround values, one of BackGround or weights must be provided
+#' @param weights a vector of weights to use for clustering, one of BackGround or weights must be provided
 #' @param nCluster number of clusters (default = 2)
 #' @param lambda weighting parameter (default = 0.1)
 #' @param nTop number of top clusters
 #' @import WeightedCluster 
 #' @export computeLandmarks
-computeLandmarks <- function(ForeGround, BackGround, nCluster = 2, lambda = 0.1, nTop = 2000){
+computeLandmarks <- function(ForeGround, BackGround = NULL, weights = NULL, nCluster = 2, lambda = 0.1, nTop = 2000){
  # check types
  stopifnot(is.matrix(ForeGround) || is.data.frame(ForeGround))
- stopifnot(is.matrix(BackGround) || is.data.frame(BackGround))
+ stopifnot(!is.null(BackGround) || !is.null(weights))
  stopifnot(is.numeric(nCluster))
  # ensure both are matrices
  ForeGround = as.matrix(ForeGround);
- BackGround = as.matrix(BackGround);
+ if(!is.null(BackGround)){
+ BackGround = as.matrix(BackGround);
+ weights = apply(BackGround, 2, median);
+ c = min(8, median(BGmedian));
+ }
+ else{
+ c = min(8, median(apply(ForeGround, 2, median)))
+ }
  # compute weighted k-medioids
  FGdist = 1 - cor(ForeGround, method = "spearman");
- BGmedian = apply(BackGround, 2, median);
- c = min(8, median(BGmedian));
- weights = 1/(1 + exp(-(BGmedian - c)/(c*lambda)));
+ weights = 1/(1 + exp(-(weights - c)/(c*lambda)));
  kMeds = WeightedCluster::wcKMedoids(FGdist, k = nCluster, weights = weights);
  kMedsCluster = kMeds$clustering;
  kMedsCluster = as.numeric(factor(kMedsCluster));