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tripal / tripal_analysis_expression

Extension module for the Tripal toolset to show differential expression data. This module was made for Drupal 7, Tripal 3, and Chado 1.3.
GNU General Public License v2.0
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hierarchical clustering for heatmaps. #210

Closed bradfordcondon closed 5 years ago

bradfordcondon commented 6 years ago

h-clustering is a requested feature for heatmaps. This means sort the features by similar expression patterns in the different biomaterials.

I'd bet plot.ly has this as an out of the box feature, and, if not, theres a plug-in. common analysis.

almasaeed2010 commented 6 years ago

There is an example in python (usually means there is an equivalent in JS) https://plot.ly/python/dendrogram/#plot-a-dendrogram-with-a-heatmap

bradfordcondon commented 6 years ago

looks to me like there is not an equivalent function. https://github.com/plotly/plotly.js/issues/1321

almasaeed2010 commented 6 years ago

This actually is possible now with plotly js:

https://plot.ly/~talgalili/23/_009681solid-cc476bsolid-99-e8b452dd3de084ea931663bbeb406a2c-0082cesolid-228b00so/#plot

Click on python & R then select Plotly.js from the dorpdown (will say JSON by default).

rgba 0 0 0 1 vs vs 15 9402241594022 vs na vs na vs 0

bradfordcondon commented 6 years ago

oh cool! I wonder if this was added recently or if i just missed it :(

On Wed, Oct 17, 2018 at 8:57 AM Abdullah Almsaeed notifications@github.com wrote:

This actually is possible now with plotly js:

https://plot.ly/~talgalili/23/_009681solid-cc476bsolid-99-e8b452dd3de084ea931663bbeb406a2c-0082cesolid-228b00so/#plot

Click on python & R then select Plotly.js from the dorpdown (will say JSON by default).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/tripal/tripal_analysis_expression/issues/210#issuecomment-430617475, or mute the thread https://github.com/notifications/unsubscribe-auth/AGvGcs0BOvH-n5LV2q4kLKqUDc_XGo1Yks5ulyk0gaJpZM4Txsfq .

-- Bradford Condon Postdoctoral Associate, Department of Ecology and Evolutionary Biology University of Minnesota http://www.bradfordcondon.com

bobbyscharmann commented 5 years ago

Does that code pen demonstration of the dendograms and heatmaps in plotly.js exist elsewhere? It no longer seems to be available from the previously mentioned source.

almasaeed2010 commented 5 years ago

Hello @bobbyscharmann

I am not sure which code pen you are referring to. We currently do not support this type of heatmap in this module since we weren't able to replicate the functionality of the code that plotly provided. As you mentioned, they've also removed the JS example and I am not sure where else to find it.

Thanks!

almasaeed2010 commented 5 years ago

Since this is marked with wontfix. I am gonna close it. Please let me know if you have any other questions.