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Visualize differentially ranked features (taxa, metabolites, ...) in tandem with log-ratios of their sample abundances
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README.md

Qurro: Quantitative Rank/Ratio Observations

Qurro logo
Build Status Code Coverage DOI PyPI

(Pronounced "churro.")

Qurro visualizes the output from a tool like Songbird or DEICODE. It displays a plot of feature rankings (either the differentials produced by a tool like Songbird, or the loadings in a compositional biplot produced by a tool like DEICODE -- when sorted numerically, either of these input types provide rankings) alongside a plot showing the log-ratios of selected features' abundances within samples.

Qurro can be used standalone (as a Python 3 script that generates a folder containing a HTML/JS/CSS visualization) or as a QIIME 2 plugin (that generates a QZV file that can be visualized at view.qiime2.org or by using qiime tools view). Starting with Qurro v0.3.0, Qurro requires a QIIME 2 version of at least 2019.7.

Qurro should work with most modern web browsers. Firefox or Chrome are recommended.

Qurro is still being developed, so backwards-incompatible changes might occur. If you have any questions, feel free to contact the development team at mfedarko@ucsd.edu.

Demos

See the Qurro website for a list of interactive demos using real datasets.

Screenshot: Visualizing KEGG orthologs in metagenomic data from the Red Sea

Screenshot showing a Qurro visualization of ranked features (which in this dataset correspond to KEGG orthologs) and a scatterplot plot of the log ratio of certain features' abundances in samples.

This visualization (which uses data from this study, with differentials generated by Songbird) can be viewed online here.

Installation and Usage

You can install Qurro using pip:

pip install numpy
pip install qurro

A python version of at least 3.5 is required to use Qurro.

Temporary Caveat

Certain characters in column names in the sample metadata, feature metadata (if passed), and feature differentials (if passed) will be replaced with similar characters or just removed entirely:

Old Character(s) New Character
. :
] )
[ (
\ |
' or " Nothing

This is due to some downstream issues with handling these sorts of characters in field names. See this issue for context.

Integration with metabolomics feature metadata

If you have a GNPS feature metadata file (where each row in the file has a parent mass and RTConsensus column), you can pass in the -gnps (--assume-gnps-feature-metadata) command-line argument to Qurro's standalone script to make Qurro understand the metadata file. Please note that this functionality is experimental; furthermore, it is not yet available in the QIIME 2 plugin version of Qurro.

Tutorials

"Moving Pictures" Tutorial

In the style of the QIIME 2 and DEICODE moving pictures tutorials, there is a draft moving pictures tutorial (showing how to use Qurro within QIIME 2, and how to interact with the generated Qurro visualization) available here. This tutorial is still a work in progress, so feel free to contact us if you have any outstanding questions (or any suggestions for improving this tutorial).

Running Qurro from the command line

Examples of using Qurro (both inside and outside of QIIME 2) are available in Qurro's example Jupyter notebooks, which are located here:

Citing Qurro

A manuscript describing Qurro is in preparation. In the meantime, you can cite the DOI of Qurro's source code (provided by Zenodo). See this link for citation instructions.

Acknowledgements

Dependencies

Code files for the following projects are distributed within qurro/support_file/vendor/. See the dependency_licenses/ directory for copies of these software projects' licenses (each of which includes a respective copyright notice).

The following software projects are required for Qurro's python code to function, although they are not distributed with Qurro (and are instead installed alongside Qurro).

Testing Dependencies

For python testing/style checking, Qurro uses pytest, pytest-cov, flake8, and black. You'll also need to have QIIME 2 installed to run most of the python tests (your QIIME 2 version should be at least 2019.7, due to the FeatureData[Differential] type being merged into q2-types starting with this release).

For JavaScript testing/style checking, Qurro uses Mocha, Chai, mocha-headless-chrome, nyc, jshint, and prettier.

Qurro also uses Travis-CI and Codecov.

Data Sources

The test data located in qurro/tests/input/mackerel/ were exported from QIIME 2 artifacts in this repository. These data are from Minich et al. 2019 [1].

The test data located in qurro/tests/input/byrd/ are from this repository. These data, in turn, originate from Byrd et al.'s 2017 study on atopic dermatitis [2].

The test data located in qurro/tests/input/sleep_apnea/ (and in example_notebooks/DEICODE_sleep_apnea/input/) are from this Qiita study, which is associated with Tripathi et al.'s 2018 study on sleep apnea [4].

The test data located in qurro/tests/input/moving_pictures/ are from the QIIME 2 moving pictures tutorial. The ordination.qza file in this folder was computed based on the DEICODE moving pictures tutorial. These data (sans the DEICODE ordination) are associated with Caporaso et al. 2011 [5].

Lastly, the data located in qurro/tests/input/red_sea (and in example_notebooks/songbird_red_sea/input/, and shown in the screenshot above) were taken from Songbird's GitHub repository in its data/redsea/ folder, and are associated with this paper [3].

Logo

Qurro's logo was created using the Lalezar font. Also, shout out to this gist for showing how to center images in GitHub markdown files (which is more of a hassle than it sounds).

Special Thanks

The design of Qurro was strongly inspired by EMPeror and q2-emperor, along with DEICODE. A big shoutout to Yoshiki Vázquez-Baeza for his help in planning this project, as well as to Cameron Martino for a ton of work on getting the code in a distributable state (and making it work with QIIME 2). Thanks also to Jamie Morton, who wrote the original code for producing rank and sample plots from which this is derived.

And thanks to a bunch of the Knight Lab for helping name the tool :)

References

[1] Minich, J. J., Petrus, S., Michael, J. D., Michael, T. P., Knight, R., & Allen, E. E. (2019). Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus. Manuscript under review.

[2] Byrd, A. L., Deming, C., Cassidy, S. K., Harrison, O. J., Ng, W. I., Conlan, S., ... & NISC Comparative Sequencing Program. (2017). Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis. Science translational medicine, 9(397), eaal4651.

[3] Thompson, L. R., Williams, G. J., Haroon, M. F., Shibl, A., Larsen, P., Shorenstein, J., ... & Stingl, U. (2017). Metagenomic covariation along densely sampled environmental gradients in the Red Sea. The ISME journal, 11(1), 138.

[4] Tripathi, A., Melnik, A. V., Xue, J., Poulsen, O., Meehan, M. J., Humphrey, G., ... & Haddad, G. (2018). Intermittent hypoxia and hypercapnia, a hallmark of obstructive sleep apnea, alters the gut microbiome and metabolome. mSystems, 3(3), e00020-18.

[5] Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., ... & Gordon, J. I. (2011). Moving pictures of the human microbiome. Genome biology, 12(5), R50.

License

This tool is licensed under the BSD 3-clause license. Our particular version of the license is based on scikit-bio's license.

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