phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
I have just posted a question regarding my heatmap but now I have another question.
I have obtained an abundance plot using this code:
BAR PLOT Tissue
top <- names(sort(taxa_sums(ps), decreasing=TRUE))#[1:100] #Uncomment this in case you want an interval
ps.top <- transform_sample_counts(ps, function(OTU) OTU / sum(OTU))
ps.top <- prune_taxa(top, ps.top)
Thing is, by including ALL data my legend is so big that I cannot possibly include it. Even not including it seems wrong, as there are countless amounts of similar colors and it is super hard to know what is happening.
Is there a way around this?
If I include the legend, I get this:
I thought that Families would not be as plentiful but maybe I should go for a higher taxonomic level like Class or Order. Do you agree? I usually see microbiome data analyses going for Family.
Someone told me I should include everything, but maybe going for the top 100 or 300 abundances could grant me readable plots.
Any thoughts on this?
I tried it and got these (the plots still need work, not sure how, though):
Hello, everyone!
I have just posted a question regarding my heatmap but now I have another question.
I have obtained an abundance plot using this code:
BAR PLOT Tissue
top <- names(sort(taxa_sums(ps), decreasing=TRUE))#[1:100] #Uncomment this in case you want an interval ps.top <- transform_sample_counts(ps, function(OTU) OTU / sum(OTU)) ps.top <- prune_taxa(top, ps.top)
plot_bar(ps.top, x="Tissue", fill="Family") + geom_bar(stat="identity", width=0.8, color=NA) + facet_wrap(~Infection, scales="free_x")
plot_bar(ps.top, x="Tissue", fill="Family") + geom_bar(stat="identity", width=0.8, color=NA) + theme(legend.position="none") + guides(fill=guide_legend(ncol=7)) + # bottom, top, left, right, none facet_wrap(~Infection, scales="free_x")
ps
Giving me this plot:
Thing is, by including ALL data my legend is so big that I cannot possibly include it. Even not including it seems wrong, as there are countless amounts of similar colors and it is super hard to know what is happening. Is there a way around this?
If I include the legend, I get this:
I thought that Families would not be as plentiful but maybe I should go for a higher taxonomic level like Class or Order. Do you agree? I usually see microbiome data analyses going for Family.
Someone told me I should include everything, but maybe going for the top 100 or 300 abundances could grant me readable plots. Any thoughts on this? I tried it and got these (the plots still need work, not sure how, though):
Thank you so much! Cheers, João Lucas