6. Visualizing the Data

Here, we can visualize the MethylationArray object with the command:

mkdir visualizations
pymethyl-visualize transform_plot -o visualizations/umap_embed.html -c disease -nn 8 

It's taking data from final_outputs/methyl_array.pkl (can be specified elsewhere using -i), finding a 3D UMAP embedding for the data using a number of neighbors (-nn) of 8. And is going to color the data using the disease column of the phenotype data. Output (-o) is a Plotly visualization that the user can interact with and explore, "visualizations/umap_embed.html".

You can overlay the age on each of the datapoints using -c Age .