diff --git a/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd b/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd index ab70a85cace8c70120839fc174d99bbaf5fdd29e..02f27bebb6d2b9e1f99a9bd791978d5ea3c99e09 100644 --- a/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd +++ b/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd @@ -843,7 +843,7 @@ set$ps.topnTax <- cuphyr::abundant_tax_physeq(ps.trans, lvl = set$taxlvl, set$my_scale_fill <- my_scale_fill -set$topntax_tb <- psmelt(set$ps.topnTax) %>% +set$topntax_tbl <- psmelt(set$ps.topnTax) %>% as_tibble() %>% left_join(set$alpha_div_ps_trans, by = "Sample") %>% select(Genus, Alias, ndvi, Abundance, Shannon) %>% @@ -853,17 +853,6 @@ set$topntax_tb <- psmelt(set$ps.topnTax) %>% arrange(ndvi) %>% mutate(ndvi_rank = c(1:length(ndvi))) -set$other <- set$topntax_tb %>% - group_by(Alias) %>% - summarise(sumabu = sum(Abundance)) %>% - mutate(Genus = 'Other', Abundance = 1-sumabu) %>% - select(-sumabu) - -set$topntax_tbl <- bind_rows(set$topntax_tb, set$other) %>% - mutate(Genus = factor(Genus, levels = c( - sort(unique(set$topntax_tb$Genus)), - "Other") - )) plots$topn_tax_custom <- ggplot(set$topntax_tbl, aes(x = fct_reorder(Alias, ndvi), y = Abundance,