To start to see patterns among cohorts in your samples, you will need to look at the sample metadata. By default, the heatmap displays only the Collection Location metadata, but you can add any metadata fields you want!
For the Feline Gingivostomatitis project, we are specifically trying to answer the question: Are there any pathogens present in cats with Feline Gingivostomatitis that are not present in healthy cats? In order to answer this question, you’ll need to add in more metadata about healthy v. diseased cats.
Between the sample names and the taxon names on the left side of the heatmap, there is a plus sign with the option to + Add Metadata. Click on the plus sign, a dropdown menu of all the metadata should appear.
Add the metadata field Diseases and Conditions by clicking on the item from the dropdown menu.
You can view the legend for each metadata field by hovering over the metadata name.
Sort the sample columns by a particular metadata field by clicking on the metadata header. Try this out for Diseases and Conditions. Notice that this separates the healthy samples in the heatmap from the stomatitis samples and allows you to more easily visualize differences in pathogen abundance between them. Note that when you sort by a metadata field, auto-clustering for samples is disabled automatically.