get_hub_plots_all_ranks: Create 5 network plots with nodes sized by hub score, 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 and sizing nodes by their hub score. MDM nodes are always featured in gray.Larger nodes indicate larger hub score value.

1	get_hub_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, resizing nodes by hub score.

`hub_plot1`	Phylum Hub Network
`hub_plot2`	Class Hub Network
`hub_plot3`	Order Hub Network
`hub_plot4`	Family Hub Network
`hub_plot5`	Genus Hub 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, point_size = hub_score(orig_graph)$vector *
                10, title = paste(met_name, rank_name2, sep = " ")) +
            theme(legend.position = "none")
        all_plots_l[[rank_name]] = g_net_plot
    }
    return(all_plots_l)
  }