Practical-3-Processing-16S-rRNA-amplicon-data.md

@@ -304,11 +304,13 @@ return(merged)
 
 Let's repeat the family level barplot with this filtered dataset
 
-```plaintext
-> marmic_filtered_family_barplot <- plot_bar(phyloseq_genus_abundant, fill="Family") +
+```
+> marmic_filtered_family_barplot <- plot_bar(phyloseq_genus_abundant, fill="Family") + facet_grid(~Sample_group, scales="free_x") + guides(fill=guide_legend(ncol=1)) + labs(y="Relative abundance", x="Sample") + theme_bw() + theme(axis.title.x = element_text(size=12,face="bold",colour="black"), axis.title.y = element_text(size=12,face="bold",colour="black"), axis.text.x = element_text(size=10, colour="black", angle=45, hjust=1), legend.title = element_text(size=12,face="bold",colour="black"), strip.background.x = element_rect(fill="white"), strip.text.x = element_text(size=11,face="bold",colour="black"))```
 ```
 
-facet_grid(<span dir="">\~</span>Sample_group, scales="free_x") + guides(fill=guide_legend(ncol=1)) + labs(y="Relative abundance", x="Sample") + theme_bw() + theme(axis.title.x = element_text(size=12,face="bold",colour="black"), axis.title.y = element_text(size=12,face="bold",colour="black"), axis.text.x = element_text(size=10, colour="black", angle=45, hjust=1), legend.title = element_text(size=12,face="bold",colour="black"), strip.background.x = element_rect(fill="white"), strip.text.x = element_text(size=11,face="bold",colour="black")) > marmic_filtered_family_barplot
+```
+> marmic_filtered_family_barplot
+```
 
 This looks much better, but it is hard to distinguish between some of the colours and also we should rearrange the sample order.