get_net_plots_all_ranks: Create network plot, with nodes colored by each...
In ConesaLab/MDM: Complete MDM Network Analysis for 16S rRNA Data

Description Usage Arguments Value Examples

Networks are created for each rank from Phylum to Genus, coloring nodes by their taxonomic classification at that rank. MDM nodes are always featured in gray.

1	get_net_plots_all_ranks(orig_graph, orig_phylo, met_name)

`orig_graph`	Network including all taxa, produced from get_back_res_meeting_min_occ function
`orig_phylo`	Phyloseq including all taxa meeting threshold, produced from get_back_res_meeting_min_occ function
`met_name`	Name of environment

Returns list of 5 ggplot objects visualizing networks at each rank from Phylum to Genus

`plot1`	Phylum Network
`plot2`	Class Network
`plot3`	Order Network
`plot4`	Family Network
`plot5`	Genus Network

##---- 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, orig_phylo, met_name)
{
    all_plots_l = list()
    for (rank_num in seq_along(colnames(tax_table(orig_phylo))[2:6])) {
        print(rank_num)
        tax_rank_names = c("Phylum", "Class", "Order", "Family",
            "Genus")
        rank_name = colnames(tax_table(orig_phylo))[2:6][rank_num]
        print(rank_name)
        rank_name2 = tax_rank_names[rank_num]
        print(rank_name2)
        g_net_plot <- phyloseq::plot_network(orig_graph, orig_phylo,
            type = "taxa", color = rank_name, label = NULL, title = paste(met_name,
                rank_name2, sep = " ")) + theme(legend.position = "none")
        all_plots_l[[rank_name]] = g_net_plot
    }
    return(all_plots_l)
  }