From 4e764427b80b077bbf40dcf2b59ee3f9e9723a22 Mon Sep 17 00:00:00 2001
From: Adrien Taudiere <adrien.taudiere@tutanota.com>
Date: Mon, 22 Jan 2024 21:46:17 +0100
Subject: [PATCH] fix : fix a bug in multitax_bar_pq

---
 R/plot_functions.R     | 2 +-
 vignettes/tengeler.Rmd | 7 +++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/R/plot_functions.R b/R/plot_functions.R
index b92327ca..65e267c4 100644
--- a/R/plot_functions.R
+++ b/R/plot_functions.R
@@ -2453,7 +2453,7 @@ multitax_bar_pq <- function(
       summarise(Abundance = sum(Abundance)) %>% 
       filter(Abundance > 0)
     
-    psm <- inner_join(psm_2, psm_1[,c("OTU", lvl1, lvl2, lvl3, fact)], 
+    psm <- inner_join(psm_2, psm_1[,c("OTU", lvl1, lvl2, lvl3)], 
                       by = join_by("OTU" == "OTU"), multiple = 
                         "first")
     
diff --git a/vignettes/tengeler.Rmd b/vignettes/tengeler.Rmd
index 57767fa2..5ee04e9e 100644
--- a/vignettes/tengeler.Rmd
+++ b/vignettes/tengeler.Rmd
@@ -6,6 +6,7 @@ vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
+
 This tutorial explore a phyloseq version of the dataset from Tengeler et al. (2020) available in the `mia` package.
 
 ```{r, include = FALSE}
@@ -158,6 +159,12 @@ biplot_pq(subset_taxa_pq(ten, taxa_sums(ten) > 3000),
 multitax_bar_pq(ten, "Phylum", "Class", "Order", "patient_status")
 ```
 
+
+```{r}
+multitax_bar_pq(ten, "Phylum", "Class", "Order", "patient_status",
+                nb_seq = FALSE, log10trans = FALSE)
+```
+
 # Differential abundance analysis
 
 ```{r}