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.
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
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.
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
z. For more information see `ili's
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
installed in QIIME 2 along with this plugin, hence we can run the following
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.