hclust size cannot be NA nor exceed 65536

[zhanghaoipp]

my dataset is 77422*207 without NA, it showed error as:

Error in hclust(get_dist(submat, distance), method = method) : size cannot be NA nor exceed 65536 Calls: draw ... make_row_cluster -> .local -> make_cluster -> hclust Execution halted

it means can not handle more than 65536 rows?

Thank you!

[jokergoo]

It is the limit of hclust(). You can sample e.g. 5000 rows from 70k rows. For the heatmap visualization, it is basically the same.

[hsiaoyi0504]

@jokergoo Looks like: https://github.com/cran/fastcluster fastcluster::hclust could help with this issue: https://github.com/jcao89757/TESSA

[BioLaoXu]

Trying to change the clustering method solves this problem，here is my code：

Heatmap(matrix =mat,
           # cluster_columns = T,
           # cluster_rows = T,
           cluster_rows = function(x){genieclust::gclust(x,distance="euclidean")},
           cluster_columns = function(x){genieclust::gclust(x,distance="euclidean")}
)