Oh awesome, thanks so much!
So, I made the heatmap with the following,
physeq %>%
tax_glom("Phylum") %>%
plot_heatmap(taxa.label = "Phylum", sample.label = "Description2", sample.order = "Type", high = "#00FFFF") +
facet_grid(~Description1, scales = "free")+
theme_q2r() +
theme(
axis.text.x=element_text(size = 6, colour = "black", angle=90, hjust=1),
axis.text.y=element_text(size = 6, colour = "black", hjust=1),
strip.text.x = element_text(size = 8, colour = "black"),
panel.spacing= unit (0, "cm")
)
and it looks something like this (I blocked some of the sensitive info),
I am looking to do two things (circled in red),
(1) Report the data is %abundance (and on a log scale... like in the tutorial)
(2) Figure out how to change the label from being just phylum to Kingdom_Phylum. Someone in another forum recommended this
newrank <- paste(physeq@tax_table [ ,"Kingdom"], physeq@tax_table [ ,"Phylum"], sep = "_") physeq@tax_table@.Data <- cbind(physeq@tax_table@.Data, newrank)
and then drawing the heatmap with the newrank taxa level, but that didn't work for some reason since it wasn't combining/collapsing the abundances within each Kingdom_Phylum.