Visualizing Microbiome Data: Choropleth Style

A Pipette and an Open Mind

Recently I’ve needed to visualize spatial changes in my microbiome data that are easily interpretable by other people. The best solution I’ve come across is simply projecting the data onto a drawing of my organism. Like this:

Zostera marina high resolution Alpha diversity of samples from pieces of a seagrass plant projected onto a drawing of that plant.

I’ve used SitePainter to produce these in the past, and in some ways it’s great. I got the figure I wanted and I’ve received a lot of positive feedback about it. The only problem is it has a steep learning curve and is the most dysfunctional GUI I’ve ever come across (generating the figure above took several days of my time, the first time). So when it became necessary to produce over forty more images like it I decided to search for a better way.

My first instinct was that there should be an easy way…

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