Beta diversity in R - what to export

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1

Hi,

I want to do my beta diversity (Bray curtis) in R. Do you know which file i have to transfer to do that in R?

Thank you

2

Hi,

I want to do my beta diversity (Bray curtis) in R. Do you know which file i have to transfer to do that in R?

Thank you

3

You could move from Qiime 2 to R at several different steps in the process.

For example, you could export your feature table, then calculate the Bray curtis beta diversity dissimilarity matrix in R and make graphs. Or you could calculate the Bray Curtis dissimilarity matrix in Qiime 2, then import the matrix and make graphs in R.

That choice is up to you!

Either way, I think the Phyloseq package is analysis like this. Check it out!
https://joey711.github.io/phyloseq/plot_ordination-examples.html

Colin

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4

Hi, thank you for your reply!
I want to use Bray Curtis to do a heatmap. So, i can download the bray curtis matrix and then export to R and do the heatmap?

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5

That's correct.

Or you can export your feature table and metadata table, and make some cool heatmaps as shown here:
https://joey711.github.io/phyloseq/plot_heatmap-examples.html

Switching from Qiime 2 to R will be a challenge, as R is pretty different. (But I think it totally worth it!) Ironically, exporting your data into R might be easier as you can more closely follow the Phyloseq tutorials.

Another option (instead of R) would be to use the underlying Qiime 2 API. This will give you the power of R and phyloseq, while being more similar to Qiime 2. Maybe someone could suggest a Qiime API tutorial to get you started!

Colin

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6

If all you want to do is generate a heatmap, this can be achieved with a few lines in python. See here:

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