I wanted to generate a heatmap on qiime2R and ran into a problem where I noticed that different feature ID have the same repeating taxon at level 5. Combined_Heatmap|690x331
It seems like the problem is rooted in the taxonomy file itself, where the classifier hasn't managed to identify different feature ID to different taxon. I'm using SILVA 132 as my classifier. SILVAtaxonomy.qza (137.6 KB)
Is there something in the Qiime2 pipeline that I have done that could cause this? Or is there a way in which I could collapse the taxonomy based on taxon at level 5 without getting rid of Feature ID and confidence that seems to be needed (?) to generate a heatmap in Qiime2R?
This might seem overly complicated, but I'm completely lost. Please let me know if anybody has any advice.
Hello!
Unfortunately, my previous answer was removed due to issues with forum updates and I do not know if you already read it or not. So I will try my best to answer it again.
It is not strange that on your heatmap taxons are repeated since you plotted it not on the taxonomy level but with features instead. Each feature (ASV, OTU) may be assigned to only to one taxon, but to each taxon numerous features may be assigned. So, in your heatmap you have several different features assigned to the same taxon - it is way they repeated.
If you will collapse your feature table to taxon, they will not be duplicated, but no feature IDs will be displayed. So, basically, you have three options:
Create heatmap only with features (no taxonomy)
Create heatmap only with taxa (no feature IDs)
Leave it as you already did - but taxons will be repeated for some features (it is not an error).
