Welcome to manta’s documentation!¶
manta: microbial association network clustering toolbox. The script takes a weighted and undirected network as input and uses this to generate network clusters. Moreover, it can generate a Cytoscape-compatible layout (with optional taxonomy input). Detailed explanations are available in the headers of each file.
manta uses the file extension to import networks. Taxonomy tables should be given as tab-delimited files. These tables can be used to generate a layout for cyjson files. Other file formats do not export layout coordinates.
manta generates a scoring matrix and uses agglomerative clustering to assign cluster identities. The scoring matrix is generated through a procedure involving network flow. Nodes that cluster separately are removed and combined with identified clusters later on. It is highly likely that networks will not converge neatly, as most real-world networks are unbalanced. In that case, manta will apply the network flow procedure on a subset of the network.
The network flow procedure relies on the following assumption: positions in the scoring matrix that are mostly positive throughout permutations, should have only positive values added. The same is assumed for negative positions. The ratio defines which positions are considered mostly positive or mostly negative.
Default numeric parameters:¶
| -min | Minimum number of clusters. Default: 2. |
| -ms | Minimum cluster size as fraction of network size. Default: 0.2. |
| -max | Maximum number of clusters. Default: 4. |
| -limit | The limit defines the minimum percentage decrease in error per iteration. If iterations do not decrease the error anymore, the matrix is considered converged. Default: 2. |
| -perm | Number of permutation iterations for network subsetting during partial iterations. Default: number of nodes. |
| -subset | Fraction of edges that are used for subsetting if the input graph is not balanced. Default: 0.8. |
| -ratio | Fraction of scores that need to be positive or negative for edge scores to be considered stable. Default: 0.8. |
| -scale | Edge scale used to separate out weak cluster assignments. The larger the edge scale, the larger the weak cluster. Default: 0.8. |
| -rel | Number of permutation iterations for reliability estimates. By default, this number is estimated from the number of dyadic pairs. |
| -e | Fraction of edges to rewire for reliability tests. Default: 0.1. |
For demo purposes, we included a network generated from oral samples of bats. This data was downloaded from QIITA: https://qiita.ucsd.edu/study/description/11815 Lutz, H. L. et al. (2018). Associations between Afrotropical bats, parasites, and microbial symbionts. bioRxiv, 340109.