Earlier I wrote a blog post about the lovely PopPUNK software, which you can read here.
Today I wanted to visualise the tree and clusters made using PopPUNK for a set of genomes, using Microreact.
Creating input files for Microreact, for an existing PopPUNK database
I followed the instructions on the PopPUNK documentation website, and ran these commands:
% poppunk_visualise --ref-db chun_poppunk_db1 --model-dir chun_poppunk_db_fitted1 --output chun_poppunk_db1_example_viz1 --microreact
where the folder chun_poppunk_db1 contained a database that I had made before (this folder contained the PopPUNK sketch files),
the folder chun_poppunk_db_fitted1 contained the fit for the database (ie. the PopPUNK clusters),
and chun_poppunk_db1_example_viz1 was the name I wanted to give to the output folder.
This produced these four output files:
chun_poppunk_db1_example_viz1_core_NJ.nwk
chun_poppunk_db1_example_viz1.microreact chun_poppunk_db1_example_viz1_microreact_clusters.csv chun_poppunk_db1_example_viz1_perplexity20.0_accessory_mandrake.dot
Visualising the PopPUNK database in Microreact
I then went to the
Microreact upload page, and uploaded the three files chun_poppunk_db1_example_viz1_core_NJ.nwk, chun_poppunk_db1_example_viz1_microreact_clusters.csv, and chun_poppunk_db1_example_viz1_perplexity20.0_accessory_mandrake.dot.
This displayed the PopPUNK database beautifully in Microreact, with a plot on the left showing how distant are the PopPUNK clusters from each other (represented in 2D space), and a tree on the right showing how the isolates are related to each other (coloured by cluster), and the key for the colour for each cluster on the far right. I love it!
Displaying additional metadata beside the tree in Microreact
I then added another file with additional metadata on MLST sequence type, and named lineage, by dragging and dropping the csv file of metadata into the 'Metadata' section of the Microreact webpage (just below the picture of clusters and tree shown above).
Then to display this metadata beside the tree in Microreact, I clicked on the 'Metadata blocks' heading in the tree section of the webpage, and chose 'cluster' and 'named lineage' and 'MLST' to display those next to the tree.
I also set the toggle for 'Leaf Labels' to 'on' in the 'Nodes and 'Labels' menu in the tree section of the webpage.
