From a594c0e446cb730980b172cc6e580225cf9058f4 Mon Sep 17 00:00:00 2001
From: Simeon <51403284+simeross@users.noreply.github.com>
Date: Thu, 13 Mar 2025 16:34:22 +0100
Subject: [PATCH] proof of principle for revision code
---
analysis/16S/16S_Analysis_pipeline_v4-3.Rmd | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd b/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd
index 02f27be..566e0f4 100644
--- a/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd
+++ b/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd
@@ -853,6 +853,13 @@ set$topntax_tbl <- psmelt(set$ps.topnTax) %>%
arrange(ndvi) %>%
mutate(ndvi_rank = c(1:length(ndvi)))
+set$other <- set$topntax_tbl %>%
+ group_by(Alias) %>%
+ summarise(sumabu = sum(Abundance)) %>%
+ mutate(Genus = 'Other', Abundance = 1-sumabu) %>%
+ select(-sumabu)
+
+set$topntax_tbl <- bind_rows(set$topntax_tbl, set$other)
plots$topn_tax_custom <- ggplot(set$topntax_tbl, aes(x = fct_reorder(Alias, ndvi),
y = Abundance,
--
GitLab