curation wine ITS1 partial

real_samples.Rmd

@@ -279,7 +279,7 @@ saveRDS(physeq_rpb2_final,"REAL_MEAT/RPB2_final.rds")
 #if (!file.exists("REAL_MEAT/meat_final.rds")){
 meat_all_final <- merge_phyloseq(physeq_its1_final, physeq_its2_final, physeq_d1d2_final, physeq_rpb2_final)
 sample_data(meat_all_final)$Marker <- factor(sample_data(meat_all_final)$Marker, levels=c("ITS1","ITS2","D1D2","RPB2"))  
-saveRDS(meat_all_final,"REAL_WINE/meat_final.rds")
+saveRDS(meat_all_final,"REAL_MEAT/meat_final.rds")
 #}else{
 #  meat_all_final <- readRDS("REAL_MEAT/meat_final.rds") 
 #}
@@ -1180,14 +1180,14 @@ ggVennDiagram(x,label_alpha = 0) +
 ## Manual curation {.tabset}
 
 ```{r, eval=T}
-#physeq_its1_final <- curation_wine_its1(physeq_its1)
-#saveRDS(physeq_its1_final,"REAL_WINE/ITS1_final.rds")
+physeq_its1_final <- curation_wine_its1(physeq_its1)
+saveRDS(physeq_its1_final,"REAL_WINE/ITS1_final.rds")
 
 #physeq_its2_final <- curation_wine_its2(physeq_its2)
 #saveRDS(physeq_its2_final,"REAL_WINE/ITS2_final.rds")
 
-#physeq_d1d2_final <- curation_wine_d1d2(physeq_d1d2)
-#saveRDS(physeq_d1d2_final,"REAL_WINE/D1D2_final.rds")
+physeq_d1d2_final <- curation_wine_d1d2(physeq_d1d2)
+saveRDS(physeq_d1d2_final,"REAL_WINE/D1D2_final.rds")
 
 physeq_rpb2_final <- curation_wine_rpb2(physeq_rpb2)
 saveRDS(physeq_rpb2_final,"REAL_WINE/RPB2_final.rds")
@@ -1197,7 +1197,7 @@ saveRDS(physeq_rpb2_final,"REAL_WINE/RPB2_final.rds")
 
 ```{r, eval=T}
 #if (!file.exists("REAL_WINE/wine_final.rds")){
-wine_all_final <- merge_phyloseq(physeq_its1, physeq_its2, physeq_d1d2, physeq_rpb2_final)
+wine_all_final <- merge_phyloseq(physeq_its1_final, physeq_its2, physeq_d1d2_final, physeq_rpb2_final)
 sample_data(wine_all_final)$Marker <- factor(sample_data(wine_all_final)$Marker, levels=c("ITS1","ITS2","D1D2","RPB2"))  
 saveRDS(wine_all_final,"REAL_WINE/wine_final.rds")
 #}else{

real_samples.html

@@ -1183,8 +1183,8 @@ ggVennDiagram(x,label_alpha = 0) +
 </div>
 <div id="manual-curation-3" class="section level2 tabset">
 <h2 class="tabset">Manual curation</h2>
-<pre class="r"><code>#physeq_its1_final &lt;- curation_wine_its1(physeq_its1)
-#saveRDS(physeq_its1_final,&quot;REAL_WINE/ITS1_final.rds&quot;)
+<pre class="r"><code>physeq_its1_final &lt;- curation_wine_its1(physeq_its1)
+saveRDS(physeq_its1_final,&quot;REAL_WINE/ITS1_final.rds&quot;)
 
 #physeq_its2_final &lt;- curation_wine_its2(physeq_its2)
 #saveRDS(physeq_its2_final,&quot;REAL_WINE/ITS2_final.rds&quot;)
@@ -1195,7 +1195,7 @@ saveRDS(physeq_d1d2_final,&quot;REAL_WINE/D1D2_final.rds&quot;)
 physeq_rpb2_final &lt;- curation_wine_rpb2(physeq_rpb2)
 saveRDS(physeq_rpb2_final,&quot;REAL_WINE/RPB2_final.rds&quot;)</code></pre>
 <pre class="r"><code>#if (!file.exists(&quot;REAL_WINE/wine_final.rds&quot;)){
-wine_all_final &lt;- merge_phyloseq(physeq_its1, physeq_its2, physeq_d1d2_final, physeq_rpb2_final)
+wine_all_final &lt;- merge_phyloseq(physeq_its1_final, physeq_its2, physeq_d1d2_final, physeq_rpb2_final)
 sample_data(wine_all_final)$Marker &lt;- factor(sample_data(wine_all_final)$Marker, levels=c(&quot;ITS1&quot;,&quot;ITS2&quot;,&quot;D1D2&quot;,&quot;RPB2&quot;))  
 saveRDS(wine_all_final,&quot;REAL_WINE/wine_final.rds&quot;)
 #}else{