README.md

QIIME 2 `ili plugin

This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.

This plugin is wrapping `ili, for more information, see https://github.com/MolecularCartography/ili.

Installation

To install q2-ili you need a working QIIME 2 installation. After you have installed QIIME 2, clone and install q2-ili by running these commands:

git clone --recurse-submodules https://github.com/biocore/q2-ili.git && cd q2-ili
pip install .
qiime dev refresh-cache

Troubleshooting installation

If the git command above results in an error like the following:

error: Server does not allow request for unadvertised object...

you may need to update the version of git that is installed on your system. You can download the latest version of git here.

Requirements

In order to use this plugin, you need a 3D model in STL format and a mapping between your samples and their coordinate locations in the model. To do this your QIIME 2 metadata file needs to include three columns labeled x, y and z. For more information see `ili's documentation.

Example

To exemplify how to use q2-ili, we will use the data from Bouslimani et al. 2015. The metabolomic features will be colored in the model according to the site where they were collected from. The data for this example is included in the example-data directory of the repository you cloned above.

First we need to import the model as a QIIME2 artifact. The type Model is installed in QIIME 2 along with this plugin, hence we can run the following command:

qiime tools import \
--type Model \
--input-path example-data/model.stl \
--output-path model.qza

Next, we generate the visualization using the model and the numeric data that we have in the metadata file:

qiime ili plot \
--i-model model.qza \
--m-metadata-file example-data/metadata.tsv \
--o-visualization visualization.qzv

Lastly, you can visualize and interact with this model using q2view.