@@ -11,3 +11,5 @@

 .Rproj.user/

 .DS_Store

+

+revdep/

@@ -2,6 +2,8 @@ CHANGES in VERSION 1.99.1

 * add `cluster_row_slices` and `cluster_column_slices` arguments in `Heatmap()`.

 * fixed a bug when annotation_height with only one annotation

+* order of k-means slices are reordered by slice mean of `row_reorder`/`column_reorder`

+  if they are provided as vectors.

 =======================

@@ -1089,7 +1089,7 @@ make_cluster = function(object, which = c("row", "column")) {

     } else {

         if(verbose) qqcat("no clustering is applied/exists on @{which}s\n")

     }

-    

+

     if(verbose) qq("clustering object is not pre-defined, clustering is applied to each @{which} slice\n")

     # make k-means clustering to add a split column

     if(km > 1 && is.numeric(mat)) {

@@ -1109,7 +1109,13 @@ make_cluster = function(object, which = c("row", "column")) {

         meanmat = do.call("cbind", meanmat)

         hc = hclust(dist(t(meanmat)))

-        weight = colMeans(meanmat)

+        # if `reorder` is a vector, the slice dendrogram is reordered by the mean of reorder in each slice

+        # or else, weighted by the mean of `meanmat`.

+        if(length(reorder) > 1) {

+            weight = tapply(reorder, cl, mean)

+        } else {

+            weight = colMeans(meanmat)

+        }

         hc = as.hclust(reorder(as.dendrogram(hc), weight, mean))

         cl2 = numeric(length(cl))