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cozygene / FEAST

Fast expectation maximization for microbial source tracking
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Adding QIIME2 plugin into FEAST_beta #8

Open cameronmartino opened 4 years ago

cameronmartino commented 4 years ago

This provides a QIIME2 plugin for the existing FEAST script. This includes tests and a pip installation.

There are multiple inputs:

  1. A feature table of counts (type FeatureTable[Frequency])
  2. A sample metadata file
  3. An environment-column of categorical type from the metadata file
  4. A source-sink-column of the categorical type used to define sources and sinks
  5. source-ids - A comma-separated (without spaces) list of ids to be defined as sources from the source-sink-column
  6. sink-ids - The same as 5 but for sinks.
  7. shared-id-column - The column of shared ids between the sources and sinks

These inputs can definitely be optimized for easier use in the future but this provides a functional solution for now.

cameronmartino commented 4 years ago

A visualization of the mixing proportions is now included with the QIIME 2 plugin through a FEAST specific barplot function. Although it produces a single stacked bar plot -- it can be split into multiple using the qiime feature-table filter-samples command. Below is the example now in the tutorial.

backhed-barplot