Show relative abundance instead of n_obs

[mhmism]

How can I show in the relative abundances for each taxa in the phylogenetic map instead of the number of observations (n_obs)?

[zachary-foster]

Hello @mhmism, sorry for the delay.

You have to use something like calc_taxon_abund to add up the abundance per OTU for each taxon. Look at this example:

https://grunwaldlab.github.io/metacoder_documentation/example.html#getting-per-taxon-information

and also at the examples in the help of "calc_taxon_abund":

library(metacoder)
?calc_taxon_abund

Let me know if you have questions

[mhmism]

Hello @mhmism, sorry for the delay.

You have to use something like calc_taxon_abund to add up the abundance per OTU for each taxon. Look at this example:

https://grunwaldlab.github.io/metacoder_documentation/example.html#getting-per-taxon-information

and also at the examples in the help of "calc_taxon_abund":

library(metacoder)
?calc_taxon_abund

Let me know if you have questions

Thanks @zachary-foster for your answer,

and in that case what would I use instead of n_obs in node_size = n_obs, in order to show nodes size according to relative abundances?

[zachary-foster]

That depends on how you do it. You will be using the contents of a column or the name of that column that contains per-taxon information. For example:

library(metacoder)
ex_taxmap$data$tax_count <- calc_taxon_abund(ex_taxmap, "abund", cols = c("count"))
heat_tree(ex_taxmap, node_label = taxon_names, node_size = ex_taxmap$data$tax_count$count, node_color = n_obs)

In this case, you have to use ex_taxmap$data$tax_count$count instead of count because there is another table with a column named count, so the function cannot tell which you mean. However, if you give it a unique name, you can do it this way:

ex_taxmap$data$tax_count <- calc_taxon_abund(ex_taxmap, "abund", cols = c("count"), out_names = c("count2"))
heat_tree(ex_taxmap, node_label = taxon_names, node_size = count2, node_color = n_obs)