Microbial association network clustering algorithm. Check out the publication for more info!
This toolbox is aimed at weighted & undirected microbial networks. It uses a diffusion-based proccess to carry out network clustering. Moreover, it can generate a Cytoscape-compatible layout that places taxonomically similar & structurally similar nodes closer together. Contact the author at lisa.rottjers (at) kuleuven.be. Your feedback is much appreciated! This version is still in early beta and has been tested for Python 3.6.
You can use conda to install manta. First add the channel hosting manta and its dependencies:
conda config --add channels ramellose
Then create a new environment containing manta:
conda create -n myenv manta
conda activate myenv
You can then call the manta command line tool from the conda environment.
To install manta locally, run:
python3 -m pip install git+https://github.com/ramellose/manta.git
To run the script, only two arguments are required: input and output filepaths. The script recognizes gml, graphml and cyjs files by their extension. By default, cyjs is exported. It also accepts text files with edge lists, with the third column containing edge weight.
manta -i filepath_to_input_network -o filepath_to_output_network
To generate a taxonomically-informed layout, add some flags:
manta -i filepath_to_input_network -o filepath_to_output_network -f cyjs --layout --central -tax filepath_to_tax_table
Layouts can only be generated for .cyjs network files, which are selected with the flag -f cyjs.
This tool can also generate cluster reliability scores by permuting the network and recomputing the clusters. The reliability scores are then calculated as confidence intervals of Jaccard Similarity indices across clusters. To use this function, you can add these flags:
manta -i filepath_to_input_network -o filepath_to_output_network -cr -rel 100
By default, manta exports a graphml file, with cluster assignments as node properties and the cluster reliability score exported as CI-related parameters. With the -f flag you can also specify other formats. With the -seed flag you can specify a random seed in case results need to be reproducible.
For a complete explanation of all the parameters, run:
manta -h
For a demo run, a network generated from fecal samples of bats has been included.
This data was downloaded from QIITA.
Lutz, H. L., Jackson, E. W., Dick, C., Webala, P. W., Babyesiza, W. S., Peterhans, J. C. K., ... & Gilbert, J. A. (2018). Associations between Afrotropical bats, parasites, and microbial symbionts. bioRxiv, 340109.
To run the demo, run manta as follows:
manta -i demo -o filepath_to_output_network
For an elaborate demo that goes through more variables, go here.
For documentation of specific functions, check out the Sphinx documentation.
An archived version of manta, together with the files used to test the algorithm, is availabe through Zenodo.
This software is still in early use. Any feedback or bug reports will be much appreciated!
- Lisa Röttjers - ramellose
See also the list of contributors who participated in this project.
This project is licensed under the Apache License - see the LICENSE.txt file for details