From 6048f14bf0c5da5cc65ccab0799218a3309c9bfe Mon Sep 17 00:00:00 2001
From: Simeon <51403284+simeross@users.noreply.github.com>
Date: Fri, 14 Mar 2025 08:44:22 +0100
Subject: [PATCH] revision 16S working
---
analysis/16S/16S_Analysis_pipeline_v4-3.Rmd | 13 +------------
1 file changed, 1 insertion(+), 12 deletions(-)
diff --git a/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd b/analysis/16S/16S_Analysis_pipeline_v4-3.Rmd
index ab70a85..02f27be 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,
--
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