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churchmanlab / genewalk

GeneWalk identifies relevant gene functions for a biological context using network representation learning
https://churchman.med.harvard.edu/genewalk
BSD 2-Clause "Simplified" License
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Visualization of the results #10

Closed chrarnold closed 4 years ago

chrarnold commented 4 years ago

Hi, I have a result table now, and I am wondering whether you or anyone else already has an R or Python script to visualize a GeneWalk result table in an automated fashion, similar to what you show in the publication. I can code it for myself, but why reinvent the wheel? :)

ri23 commented 4 years ago

Hi @chrarnold , yes I can provide you some Python code to plot GO relevance scores bar charts for individual genes. I am thinking to add this to the GeneWalk tutorial http://churchman.med.harvard.edu/genewalk to make it easily accessible to the public. I will work on that, thanks

chrarnold commented 4 years ago

I think this would be great and contribute largely to the success and usability of the tool. I am an R guy, I will try to add some R code. I am happy to share this once I have something nice.

chrarnold commented 4 years ago

But please share the Python code also, the Documentation sounds like the right place to do so. Honestly, an automated visualization as part of the genewalk workflow would be great also, so users can directly visualize the results, in addition to the output table. Like a PDF with one page per gene or something, just something to get you started and excited. Similar visualizations than you used in the paper essentially.

ri23 commented 4 years ago

The tutorial now has bar chart visualization Python code in a short jupyter notebook http://churchman.med.harvard.edu/genewalk We'll look into more automated visualization scripts at a later time.

chrarnold commented 4 years ago

Hi, I invested an hour yesterday to produce an R script that takes an output table from GeneWalk and mimics the plots you produced for the paper. It goes even a bit further and varies the fdr thresholds etc. Are you interested in having it and sharing it in the Tutorial?

ri23 commented 4 years ago

Thank you for the suggestion to support plotting for R users. I have made some code to plot the same bar charts in R with ggplot2 in the tutorial. I kept it very similar to the Python code for simplicity.

bgyori commented 4 years ago

The tutorial now covers visualization with code samples in R and Python - should we close this issue?