The Map Viewer

The Map Viewer is designed for interactive exploration of tSNE submaps at the single cell level, with the following features:

• Metadata on each cell can be viewed by scrolling with the mouse wheel while hovering over the Metadata text box. This will bring up a legend box with the metadata items in that particular submap.

• tSNE maps can be recomputed on the fly, and paused during computation for detail inspection and analysis. Note that linear structures during A-tSNE computation with exponential force decay have been shown to suggest differentiation pathways and lineage relations.

• Expression of an arbitrary gene can be painted in the map by starting to type the gene name in the expression text box, and selecting the target gene from the drop down menu.

• Hovering over a cell brings up an information panel with the detail metadata on each nucleus.