Hi there R wizars!!
I'm ew in all this R analysis. I was wondering if it is possible to get a heatmap with the significance symbols from a qiime2 (phyloseq) file.
I got the heatmap with the following script:
library(qiime2R)
physeq<-qza_to_phyloseq(
features="table5.qza",
tree="rooted_tree.qza",
taxonomy="taxonomy.qza",
metadata="metadata.tsv"
)
library(microbiome)
physeq.genus = aggregate_taxa(physeq, level = "Genus")
N=101
top.genus.names = names(sort(taxa_sums(physeq.genus), TRUE)[1:N])
top.genus.names
top.genus.names = top.genus.names[2:N] #Eliminamos los unknown, asegurarse que estan en la posicion 1
top.genus = prune_taxa(top.genus.names, physeq.genus)
top.genus.rel = transform_sample_counts(top.genus, function(x) x / sum(x) )
metadata = read_q2metadata("metadata.tsv")
plot_heatmap(top.genus.rel, distance = "bray", sample.label="Tillage", sample.order="Tillage", taxa.label="Genus", taxa.order="Phylum", low="#ABECE8", high="#0F27A1", na.value="white", title = "Top100 genus") +
facet_grid(~ Date, scales = "free_x")
But I also want to add the significances differences and, if it is possible, to get just one column per Sampletype instead of one column per sample.
Thank you in advance.
Sincerely, Ana.