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tk382 / HIPPO

Heterogeneity Induced Pre-Processing tOol
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Add algorithm options for Kmeans #2

Open tk382 opened 4 years ago

tk382 commented 4 years ago

To avoid the following Quick TRANSFERing error https://stackoverflow.com/questions/21382681/kmeans-quick-transfer-stage-steps-exceeded-maximum add user-option to choose "MacQueen" or "Lloyd".

tk382 commented 4 years ago

Also, add functionalities for different clustering methods than K-means. For example, Louvian or Leiden.

shanzhyang commented 4 years ago

Hi, i found only "Seurat" and "SC3" can be found as options of the clustering methods. So the Seurat is louvian and SC3 is Leiden? Thanks!

tk382 commented 4 years ago

Yes - the original hippo function uses 'PCA+kmeans' (parameter 'kmeans'), but it can also directly calls the function from the Seurat and SC3 package that use Louvain and Leiden respectively. Thanks.