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 file and <ST>_phylogeneticTree.newick files. PhyloPHoeNIx will change the first column of you 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 popup 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.
A new popup 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.
