Temporal dynamics of microbial mats a network based approach
Microbial mats from Churince Supplementary Information
Supplementary Information
Repository that contain the main data and scripts to recompute the figures from:
De Anda V, Zapata Peñasco I, Blaz J, Poot-Hernandez AC, Contreras Moreira B, Gonzales Laffite Marcos, Hernandez Rosales M, Gamez Tamariz N, Eguiarte Fruns E, Souza V. Understanding the mechanisms behind the response to environmental perturbations in microbial mats: a metagenomic-network based approach Front. Microbiol. 9:2606. doi: 10.3389/fmicb.2018.02606
Last updated: 11/29/2018
To reproduce the figures first install jupyter notebook and then clone the repository.
git clone https://github.com/valdeanda/Time_series_mats.git
cd scripts
ipython3 notebook
Requirements
In order to reproduce all the figures the following libraries and packages must be installed first
Python
- Pandas >= 0.20.3
- Numpy >= 1.13.3
- Seaborn >= 0.8.0
- Matplotlib >= 2.02
R packages
- Phyloseq
- ggplot2
- vegan
- pvclust
- devtools
- fpc
Figures
Taxonomic composition, microbial mat core and rare biosphere
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To compute the ecological indexes plase open the following script directly in your browser.
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To obtain the final figure
The script is available in notebook format
jupyter notebook Diversity.ipynb
Presence absence profile with get_homologues
- To compute the microbial mat core and the presence absence profile of each site we used get_homologues. The script is available in notebook format. To repeat the analysis please type in your terminal:
jupyter notebook Core_bacteria.ipynb
Capturing the dynamics of biogeochemical cycles with MEBS
- Frist compute MEBS with the following script in notebook format.
jupyer notebook MebsInTime.ipynb
- Then compute the metbolic completeness
Script available in notebook format.
jupyter notebook completeness.ipynb
Networks
Open the following script directly in R
The dynamic networks for each site are available here:
Network motifs
Script available in notebook format.
jupyter notebook Motifs.ipynb
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