PluMA plugin to take a weighted network and run Markov Clustering (van Dongen, 2000). The plugin accepts as input a CSV file representing the network, with nodes represented as both rows and columns and entry (i, j) is the weight of the edge from node i to node j. The plugin then outputs clusters as separate CSV files using the output prefix, in the following format:
"","x" "1","Family.Porphyromonadaceae.0005" "2","Family.Porphyromonadaceae.0006" "3","Family.Lachnospiraceae.0045" "","x" "1","Family.Lachnospiraceae.0001" "2","Family.Lachnospiraceae.0002" "3","Family.Lachnospiraceae.0007" "4","Family.Lachnospiraceae.0013" "5","Family.Ruminococcaceae.0003" "6","Family.Lachnospiraceae.0018" "7","Family.Ruminococcaceae.0006" "8","Family.Lachnospiraceae.0044" "9","Order.Clostridiales.0004" "10","Family.Lachnospiraceae.0057" "11","Dorea.0001" "12","Oscillibacter.0004"
Note each cluster is separated by the delimiter "","x".
Updated August 2019: The plugin has been extended for first- and second- level clustering First-level clustering files end with *.1.csv and second-level with *.2.csv Individual cluster data is also output with the second-level clustering