Calculation of median relative abundance
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Entering edit mode
2.4 years ago
MSRS ▴ 580

Hi,

I am feeling trouble in median relative abundance in microbiome analysis.

ps.rel = transform_sample_counts(ps, function(x) x/sum(x)*100)
# agglomerate taxa
glom <- tax_glom(ps.rel, taxrank = 'Phylum', NArm = FALSE)
ps.melt <- psmelt(glom)
# change to character for easy-adjusted level
ps.melt$Phylum <- as.character(ps.melt$Phylum)

ps.melt <- ps.melt %>%
group_by(body.site, Phylum) %>%
mutate(median=median(Abundance))
# select group median > 1
keep <- unique(ps.melt$Phylum[ps.melt$median > 1])
ps.melt$Phylum[!(ps.melt$Phylum %in% keep)] <- "< 1%"
#to get the same rows together
ps.melt_sum <- ps.melt %>%
group_by(Sample,body.site,Phylum) %>%
summarise(Abundance=sum(Abundance))

ggplot(ps.melt_sum, aes(x = Sample, y = Abundance, fill = Phylum)) +
geom_bar(stat = "identity", aes(fill=Phylum)) +
labs(x="", y="%") +
facet_wrap(~body.site, scales= "free_x", nrow=1) +
theme_classic() +
theme(strip.background = element_blank(),
axis.text.x.bottom = element_text(angle = -90))


Here, median relative abundance calculation (< 1% indicates the rare taxa in each group, with median relative abundance < 1%) is difficult to understand to me. Can anyone please explain it?

R • 988 views
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Entering edit mode

Thank you so much. Got it. It was by group median.