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grunwaldlab / analysis_of_microbiome_community_data_in_r

This is the source code for the "Analysis of Microbiome Community Data in R" ICPP 2018 workshop. The website is available at: https://grunwaldlab.github.io/analysis_of_microbiome_community_data_in_r/
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Stacked Bar Plots and other Stats #16

Open Nwilliams96 opened 4 years ago

Nwilliams96 commented 4 years ago

Hi,

Are you planning on making more workshops? If so I would love to know how to make a stacked Stacked bar chart from the obj. I would also love to go beyond alpha and beta diversity and to make some CCA plots and do SIMPER analysis. I am new to this so sorry if what I'm asking doesn't make sense or if this isn't the appropriate place to ask.

Thank you for the workshop you have created though, it is very useful!

Kind regards, Nate

zachary-foster commented 4 years ago

Hi Nate,

Yes, this is the good place to ask, although the newest version of the documentation is here:

https://github.com/grunwaldlab/metacoder_documentation

https://grunwaldlab.github.io/metacoder_documentation/

We are doing another workshop in December and I can add some info on stacked bar charts. I will have to look more into SIMPER analysis. Anything I add will be at https://grunwaldlab.github.io/metacoder_documentation/.

Keep in mind that the abundance matrix stored in a taxmap object is just a table, so you can follow any tutorial that uses an abundance matrix. You can get the table using obj$data$my_table. You might have to transpose the matrix with t, to use some software that expects taxa to be columns (e.g. vegan).

Thanks!