Hello,
I encountered the following error when using my picrust2 output within R:
The kegg pathway with zero abundance in all the different samples has been removed.
Error in pathway_daa(abundance = abundance, metadata = metadata, group = group, :
object 'p_values_df' not found
I followed the walkthrough (code below) but I'm getting an error that I can't quite make sense of. Could this be something with my file format/code or is there another input component I need to include in my R code? Thank you.
meta<-read_delim("meta.tsv", delim = "\t", escape_double = FALSE)
group<- "site"
daa_results_list<- ggpicrust2(
file = "pred_metagenome_unstrat.tsv",
metadata = meta,
daa_method = "linDA",
group = "site",
pathway = "KO",
p_values_bar = TRUE,
ko_to_kegg = TRUE,
order = "pathway_class",
x_lab = "pathway_name",
select = NULL,
reference = NULL
)
Thanks!