Dependency: Requires SIMLR package, and specifically references projsplx_R.so. SIMLR is available at: https://github.com/BatzoglouLabSU/SIMLR. This file can be placed in the PluMA root directory
PluMA plugin to cluster a network using the Single-Cell Interpretation via Multiple Kernel Learning (SIMLR, Wang et al. 2017).
The plugin accepts input as a CSV file where rows and columns each represent nodes, and entry (i, j) corresponds to the weight of the edge from node i to node j.
The plugin will generate clusters in two formats: NOA and CSV. The user provides the prefix for the output files in the configuration file, which will then generate files prefix.csv and prefix.noa.
The cluster CSV file will take the following format:
"", "x" "1",Family.Lachnospiraceae.0091 "2",Class.Clostridia.0003 "3",Family.Lachnospiraceae.0093 "4",Family.Lachnospiraceae.0094 "", "x" "1",Family.Lachnospiraceae.0006 "2",Lactobacillus.0002 "3",Family.Porphyromonadaceae.0009 "4",Family.Lachnospiraceae.0008 "5",Family.Lachnospiraceae.0009 "6",Lactobacillus.0003 "7",Oscillibacter.0002 "8",Family.Ruminococcaceae.0001 "9",Family.Porphyromonadaceae.0016 "10",Atopostipes.0001 "11",TM7_genus_incertae_sedis.0004 "12",Clostridium_XlVa.0003 "13",Family.Lachnospiraceae.0106 "", "x" "1",Kingdom.Bacteria.0007 "2",Order.Clostridiales.0017 "3",Phylum.Firmicutes.0003 "4",Family.Ruminococcaceae.0024 "5",Family.Lachnospiraceae.0092
Note that each cluster is separated by a line "", "x"
The other output file is a NOde Attribute (NOA) file for Cytoscape, which is just a table with each node name and the cluster to which it belongs:
Name Cluster Family.Porphyromonadaceae.0001 23 Family.Porphyromonadaceae.0002 23 Family.Porphyromonadaceae.0003 18 Bacteroides.0001 6 Alistipes.0001 6 Family.Porphyromonadaceae.0004 6 Barnesiella.0001 9 Family.Porphyromonadaceae.0005 6 Lactobacillus.0001 18 Family.Lachnospiraceae.0001 18 Family.Porphyromonadaceae.0006 16 Family.Lachnospiraceae.0002 18 Kingdom.Bacteria.0001 21
This cluster then becomes an attribute of each node in Cytoscape, and can be used for further downstream analysis and visualization.