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biocore / microsetta-interface

The Microsetta participant facing user interface
BSD 3-Clause "New" or "Revised" License
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[Beta diversity] page specific updates #95

Open wasade opened 3 years ago

wasade commented 3 years ago

Stop mentioning QIIME2 without explaining it. Is it important that it is on this page?

“Everything after the first sentence explains the math/reasoning behind the chart but I still don’t know what I’m supposed to be looking at or how to read it.”

The emperor plot is confusing. This should be relegated to an "advanced" tab with further text about how to use it. In replacement, we should include a few non interactive 2D scatters colored by age and BMI if only fecal, or body site if multiple body site and study 10317, or country if fecal and multiple study, or body site if multi site and multiple study

wasade commented 3 years ago

@gwarmstrong, are we setup to also easily produce 2D scatters from the results API?

gwarmstrong commented 3 years ago

The emperor endpoint should be sufficient for making scatters like described above, but it could require iterating over some arrays to switch from a row-oriented representation to a column-oriented representation. Also, IIRC, it might send a bunch of extra data over the wire, depending on the number of columns in the pcoa artifact. It would be pretty straightforward to add a flag that lets you pare down the PCoA to the desired number of dimensions.

wasade commented 3 years ago

Okay. If there is something pretty, simple and engaging without much new dev effort, then let's do that. Thanks!!

wasade commented 3 years ago

Comments from Justin

- i suggest to hyphenate all instances of alpha-diversity and beta-diversity
- i think the phrase 'differing in how to weight the distance between any two microbes' should be 'differing in how to weight the distance between any two samples'
- i suggest to replace 'evolutionary distance' with 'evolutionary relationships'
- i suggest to add instructions on how to manipulate the plot, ideally above the figure. It can be very simple. E.g., Click and scroll on the plot below to move and zoom around it.
- i suggest to explain the figure in the text above it. It can be very simple. E.g., In the image below, each point represents a sample, and samples are separated based on differences in the presence of bacterial and archaeal taxa.