Commit 2b0792da authored by Olivier Rue's avatar Olivier Rue
Browse files

curation wine ITS1 partial

parent 1fef5a43
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......@@ -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{
......
......@@ -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{
......
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