func_ids option? and dowstream analysis & plotting?

[marwa38]

thanks very much for how straightforward to run your code
regarding the comment from R after running beta_div_contrib()
what is expected to be in func_ids?

by the way, I didn't get any table outputs from this chunk although I got a directory output,
Any comments on how I could plot all tables significant functions (each function is in a table).

Is any advice or workflow available on downstream analysis of contributional alpha diversity? (if possible other than STAMP since it hasn't been updated since 2015)
Thanks in advance

[gavinmdouglas]

Hi @marwa38,

You can see all the option documentation by typing ?beta_div_contrib. For func_ids it says: character vector specifying subset of function ids to include for analysis. Will analyze all functions present if this is not specified, i.e., these are the ids of the functions to use for the analysis.

The function will either return an object containing all distance matrices (return_objects option), or write them out as files (write_outfiles option). This distinction is made because the size of the return object can really be gigantic, and so writing individual tables to the disk separately can be much more memory efficient, depending on how many samples and functions are input.

My personal preference is to conduct data analysis in R using the ggplot2 package and other great packages like complexHeatmap.