Question

ComplexHeatmap - Default distance and hierarchical clustering methods

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Katharina • 0

@c1cc8b34

Last seen 18 months ago

Berlin

Hello everyone,

as it is possible to specify the distance method (euclidian, pearson,..) and hierarchical clustering method (single, complete...) with ComplexHeatmap, I was wondering about the default settings in case I don't specify them myself?

Thanks a lot for your help.

ComplexHeatmap Complex • 4.3k views

ADD COMMENT • link updated 22 months ago by elefth.pavlos ▴ 40 • written 22 months ago by Katharina • 0

score 2 · Accepted Answer · 2023-01-25

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Basti ▴ 780

@7d45153c

Last seen 9 hours ago

France

Default settings are "euclidean" and "complete" : https://github.com/jokergoo/ComplexHeatmap/blob/f6edeaa1241159119590a604ccd1f5b82a69b60e/man/Heatmap.Rd

ADD COMMENT • link 22 months ago Basti ▴ 780

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If you are answering a question, please use the ADD ANSWER button rather then ADD COMMENT so people know the question has been answered.

ADD REPLY • link 22 months ago James W. MacDonald 67k

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Thank you very much, Basti! Do you know if it is the same for gplots::heatmap.2?

ADD REPLY • link 22 months ago Katharina • 0

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Hi Katharina,

Default settings are same as with the ComplexHeatmap function, "euclidean" for the distance and "complete" for the method.

Check the following link for the heatmap.2 documentation, this one for the distfun argument and also here for the available hclustfun methods of heatmap.2 function.

ADD REPLY • link 22 months ago elefth.pavlos ▴ 40