get_graph_wo_unk: Create igraph object without MDM nodes at each rank
In ConesaLab/MDM: Complete MDM Network Analysis for 16S rRNA Data

Description Usage Arguments Value Examples

For each taxonomic rank, all taxa designated as MDM are removed from the original network (igraph) using names of the MDM found by the met_wo_unk function. A new network (igraph) for each rank is produced, where only taxa with known taxonomic classification are present.

1	get_graph_wo_unk(orig_graph, met_wo_unk)

`orig_graph`	Network (graph) of all taxa, including MDM
`met_wo_unk`	List of 7 otu tables, produced from met_wo_unk function, each corresponding to the taxa with known classification at that rank. Each OTU table shows the taxa ids and counts for these known taxa.

Returns List of 7 igraph objects.

`wo_unk_graph1`	Network (igraph) of taxa with known Kingdom classification
`wo_unk_graph2`	Network (igraph) of taxa with known Phylum classification
`wo_unk_graph3`	Network (igraph) of taxa with known Class classification
`wo_unk_graph4`	Network (igraph) of taxa with known Order classification'
`wo_unk_graph5`	Network (igraph) of taxa with known Family classification
`wo_unk_graph6`	Network (igraph) of taxa with known Genus classification
`wo_unk_graph7`	Network (igraph) of taxa with known Species classification

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (orig_graph, met_wo_unk)
{
    wo_unk_graph_l = list()
    for (name in names(met_wo_unk)) {
        print(name)
        tax_level = name
        wo_unk_graph <- igraph::delete_vertices(orig_graph, which(!names(V(orig_graph)) %in%
            rownames(met_wo_unk[[tax_level]])))
        print(wo_unk_graph)
        wo_unk_graph_l[[name]] = wo_unk_graph
    }
    return(wo_unk_graph_l)
  }