Understanding plot_heatmap results (phyloseq)

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2.9 years ago

poltora4enko ▴ 10

Hello dear colleagues! I'm a student. And i just started learning these methods. Could someone help me understand some of the details on this plot:

Why species are repeated on axis y?
What do the gaps between species on the same axis mean?

It's a metagenome of fungi on grapes. Thanks for any help!

top100ITSsklearn <- names(sort(taxa_sums(ITSsklearn), decreasing=TRUE))[1:20]

ITSsklearn.top20 <- transform_sample_counts(ITSsklearn, function(OTU) OTU / sum(OTU))

ITSsklearn.top20 <- prune_taxa(top20ITSsklearn, ITSsklearn.top20)

plot_heatmap(ITSsklearn.top20, method = "MDS", taxa.label = "Species", trans = NULL, low = "beige", high = "red", na.value = "beige", distance = 'bray')+ theme (axis.text.y = element_text(size=16))

enter image description here

heatmap phyloseq • 1.3k views

ADD COMMENT • link updated 2.9 years ago by lagartija ▴ 160 • written 2.9 years ago by poltora4enko ▴ 10

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Do you have any "NA" in your ITSsklearn ? And what is in top20ITSsklearn ? Maybe you could show us part of the raw data that you used to make your phyloseq object.

ADD REPLY • link 2.9 years ago by lagartija ▴ 160

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