revision 16S working

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,