qzv-viewer

This is a simple package allowing you to view QIIME2 visualisers (files ending with .qzv) in notebooks. Currently, only Jupyter notebook viewer allows you to view all types of QIIME2 visualisers correctly. In the VSCode notebook viewer only non-emperor plots are supported with an additional clean-up step required after the plot.

Install

We recommend using the functonalities in a conda environment with the required dependencies installed within:

conda create -y -n qzv-viewer
conda activate qzv-viewer

conda install \
  -y -c conda-forge -c bioconda -c qiime2 -c defaults \
  qiime2 q2cli xmltodict jupyter

Now install qzv-viewer within:

pip install git+https://github.com/adamovanja/qzv-viewer.git

Jupyter Notebook Demo

To run the demo in jupyter notebook, clone into the repository:

git clone https://github.com/adamovanja/qzv-viewer.git

and open the demo notebook:

cd qzv-viewer/src/tests/
jupyter notebook demo_jupyter.ipynb

VSCode Notebook Demo

To run the demo in VSCode, clone into the repository:

git clone https://github.com/adamovanja/qzv-viewer.git

and open the demo notebook:

cd qzv-viewer/src/tests/
jupyter notebook demo_vscode.ipynb

As you can see there is currently an additional clean-up step required in VSCode after viewing the visualisations.

Contact

In case of questions or comments feel free to raise an issue in this repository.