How to get started with the UMAP
The UMAP plot contains dots that represent either species, in the species tab or protein domains, in the domains tab. Mouse over a dot to identify it. Draw a box (holding down the mouse) around a group of dots to zoom in and better identify them. The taxonomy for the species in focus is shown at the top of the screen. Click on a dot to freeze the taxonomy in place. You can then select one to show all members of the selected taxonomy.
Drawing shapes and selecting regions
Drawing a box is not the only way to select a region. The lasso tool allows you to select an odd shaped region to include and exclude dots outside of a box shape. The number of points selected is shown at the bottom of the plot. Once a selection is made, click the 'Show Selected Species' to see the names, statistics on the domains found in the selection relative to the entire population in the map, and phylogenetic trees in two forms.
Searching by species
Use the search box to type in the name of a species and the available selections will appear in a list. Select your species of interest and click the "Show" button to redraw the map. The searches species are now indicated by colors in the legend and the map.
Searching by domains to find matching species
Selecting domains to see domain counts in species
When using the domains tab, search for domains of interest to locate them in the map. Then select a cluster around your domain of interest and scroll to the bottom of the page to identify the members, and click the "count distributions" button. This presents a page (it may take several seconds to load) showing species that contain a summed count of the domain selection that as above your selected threshold. Each domain count is found for each species in a table below the map. And below each one is a listing of the count groups as shown in the map.
Comparing 2 regions of selected species statistically
The compare page allows the user to select regions of species from two identical umaps. T-scores are determined for all PFAM domains in each group's population of species and compared.
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