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Add a possibility to easily combine matshow with dendrogram to create an R-style heatmap #2456

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oxananu opened this Issue Sep 24, 2013 · 2 comments

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oxananu commented Sep 24, 2013

It would be nice to have an easy way of plotting an R-style heatmap using matplotlib. A plot like this is useful when visualizing hierarchical clustering results.

An example of how it can be done in Python now: http://altanalyze.blogspot.se/2012/06/hierarchical-clustering-heatmaps-in.html

Heatmap function in R:
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/heatmap.html

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tacaswell Jan 17, 2014

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Related to #1257 . I suspect the tree-generation code will be the same in both.

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tacaswell commented Jan 17, 2014

Related to #1257 . I suspect the tree-generation code will be the same in both.

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petehuang Dec 30, 2016

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This hasn't been updated in a while. There has been no movement on the related issues. PRs still welcome, it'd be cool to see!

The example code linked the original post can be found here: http://code.activestate.com/recipes/578175-hierarchical-clustering-heatmap-python/

The dendrogram comes from scipy.cluster.hierarchy so I'm wondering what the solution in matplotlib would look like to take that as input.

Recommend labeling as Difficulty: Medium?

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petehuang commented Dec 30, 2016

This hasn't been updated in a while. There has been no movement on the related issues. PRs still welcome, it'd be cool to see!

The example code linked the original post can be found here: http://code.activestate.com/recipes/578175-hierarchical-clustering-heatmap-python/

The dendrogram comes from scipy.cluster.hierarchy so I'm wondering what the solution in matplotlib would look like to take that as input.

Recommend labeling as Difficulty: Medium?

@tacaswell tacaswell modified the milestones: 2.1 (next point release), 2.2 (next next feature release) Oct 3, 2017

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