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MD-Anderson-Bioinformatics / NGCHM-R

An R library for creating Next-Generation Clustered Heat Maps (NG-CHM)
http://bioinformatics.mdanderson.org/main/NG-CHM-V2:Overview
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No "centroid linkage" agglomeration method available for hierarchical clustering #40

Open monikaramos opened 9 months ago

monikaramos commented 9 months ago

Hi there,

In the documentation for using the NGCHM builder, it states: "Agglomeration Method This is applicable only when rows are ordered by hierarchical clustering and describes the algorithm used for clustering. The currently supported methods are: Average Linkage, Complete Linkage, Single Linkage, Ward, Mcquitty, Median, or Centroid."

However, the actual builder doesn't have centroid linkage as an agglomeration option. Can this be added?

Thank you!

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marohrdanz commented 3 months ago

Hi @monikaramos. Sorry for the documentation confusion and the very late response.

The R package (this repo) supports these methods (because it uses stats::hclust()), but unfortunately we don't have immediate plans to add these features to the GUI builder. We've updated the documentation to be more clear.

Are you able to use the R package to build your NG-CHMs?