mikemc / speedyseq

Speedy versions of phyloseq functions
https://mikemc.github.io/speedyseq/
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Add method to facilitate using dplyr::count on tax tables and sample data #73

Open mikemc opened 3 years ago

mikemc commented 3 years ago

Problem: Currently one needs to do

GlobalPatterns %>% sample_data %>% as("data.frame") %>% count(SampleType)

This isn't so bad, but it's annoying to have to always explicitly coerce to a data frame.

If we could define count() methods for sample_data and tax_table objects, then we could just omit that step. However, I haven't figured out how to define methods for S4 objects in a way that doesn't interfere with dplyr's functions (hence why we now have ps_tibble() instead of just as_tibble() methods). An alternative would be to go the route of the other dplyr verbs and define count_sample_data() and count_tax_table() functions.

ps %>% count_sample_data(SampleType)