Visualizing PhyloPHoeNIx Output
PhyloPHoeNIx output seamlessly integrates into Microreact through their upload portal. There are up to 3 files you can upload directly from PhyloPHoeNIx output folder to Microreact:
- <ST>_clean_metadata.tsv
- <ST>_phylogeneticTree.newick
- <ST>_snvMatrix.tsv
Drag and drop these files into the upload portal. Make sure you set the file kind of <ST>_snvMatrix.tsv to matrix so MicroReact knows how to handle it.
Click "Continue" on the pop-up window(s) to confirm that WGS_ID is the ID column for <ST>_clean_metadata.tsv and <ST>_phylogeneticTree.newick files. PhyloPHoeNIx will change the first column of your input metadata file to WGS_ID to make sure this is consistent.
To see the isolate names on the tree, click the "Nodes & Labels" drop-down menu in the "Tree" window and turn on the "Leaf Labels" option.
To make the matrix easier to assess, click the "Labels" drop-down menu in the "Matrix" window and turn on the "Show Values" option.
If you provided dates and want to add a timeline to the Microreact window, start by clicking the white pencil icon on top right corner of the website. A square window outline will appear, drag and drop the window wherever you want to have the timeline displayed in the Microreact window. Next, in the drop-down menu click on "Create new Timeline".
A new pop-up window will appear and you need to select "One Column: Formatted Values" as all the date information is in one column. Next, in the "Temporal Data Column" click "date" so that we tell Microreact that our timeline information is in the "date" column.
By default, Microreact colors the isolates in all windows by the first column in the metadata file which should be "FastANI_Organism" or "" as this is information added by PhyloPHoeNIx. To change this, start by clicking the white "eye" icon on the top right of the Microreact window. A drop-down menu will appear and once you click on "Colour Column" you will see the choice of all columns in your metadata column to pick from that will color your isolates by.
