I would like to kindly ask you for your help. I am currently using Graphlan and I want to plot the phylum, family and genera to the tree (–annotations 2,5,6) but only shows the family and genera level.
I used the following for the annotation
export2graphlan.py -i Tk.Met.metaphlan.format.taxonomy.txt --tree Tk.Met.tree.txt --annotation Tk.Met.annot.txt --most_abundant 60 --abundance_threshold 3
–least_biomarkers 10 --annotations 2,5,6 --external_annotations 7 --min_clade_size 1 --ftop 200 --title “TK Gut Metagenome”
The annotation and tree file (.txt) and the figure are attached. Could you please help me to solve this issue?
Thanks a lot for your help!
Tk.Met.annot.txt (16.1 KB)
Tk.Met.tree.txt (15.3 KB)