Creating Alpha Diversity Plot in R with Qiime output

[Sofia P]

I would like to make a plot like the alpha diversity plot in 5.1 seen here http://buff.ly/29ePoIK)
I have run Qiime and have text files of the rarified values (alpha_div_collated files) for the shannon index, PD, observed and chao1 (attached here.)  I am not sure how to combine these and create the plot as in the link since I'm taking the externally generated results.   Any suggestions on how to plot this data in R? 

Best, 

Sofia 

[Colin Brislawn]

Hello Sofia,

This forum is more focused on supporting qiime software, not other programs like Phyloseq. That being said, I have used phyloseq and may be able to help you get started.

Have you taken a look at the qiime tutorial about importing data? I think you may have better luck by trying to import your .biom file into phyloseq, then making the graphs. Doing stats in qiime then just using R for graphing could be a little harder, and will not be covered by the standard tutorials.

https://joey711.github.io/phyloseq/import-data 

I hope this helps. If you have additional questions about phyloseq, you could try posting an issue on the official phyloseq issue tracker: https://github.com/joey711/phyloseq/issues 

Have a good weekend!

Colin

[Sofia P]

Thank you very much for your help Colin! The links are useful :) 

Hope your weekend was good! 

Best, 

Sofia 

[Sofia P]

One other question, is there another way then, to change the appearance of the graphs from qiime, so that they look better in papers?

BR, 

Sofia 

[Colin Brislawn]

Hello Sofia,

Qiime 1 does not support a really robust way of modifying and refining plots. This sort of interactive visualization is one of the core goals of qiime 2: 

"We have not decided on the interactive visualization framework at this time, but we are exploring Jupyter’s interactive widgets, Bokeh, Seaborn, and others."

https://qiime.wordpress.com/2015/10/30/toward-qiime-2/

Phyloseq makes use of the ggplot2 package in R which is highly customizable.

https://joey711.github.io/phyloseq/plot_ordination-examples 

Colin

[Sofia P]

Thanks again Colin, great links! 

BR, 

Sofia