agglomerateByRank help

[kusandeep]

Hi, I wanted to explore family-level abundance density, and for that, I used the code below. v5v7_TSE_family <- v5v7_TSE %>% agglomerateByRank(rank = "Family")

plotAbundanceDensity(v5v7_TSE_family, layout = "jitter", abund_values = "relabundance", n = 10, point_size=1, point_shape=19, point_alpha=0.3) + scale_x_log10(label=scales::percent)

However, when I agglomerate by family, seems like there are some uncultured "families" from different or same "Orders" agglomerating together and creating probably a false family (see the plot below)?. Any suggestion on how to deal with them? One thought I had was to agglomerate by string up to Family to keep the uniqueness and show the whole string from Phylum up to family or genus. Function similar to 'microbiomeutilities::format_to_besthit'