Looking for 2D Point Cloud Labeling tool

Trying to understand my high-dimensional Dataset I am using t-SNE to project the data onto two dimensions. As is the nature of t-SNE, this will be an experimental, iterative process.

I want to be able to keep track of datapoints movements over many iterations. For that I am searching for a tool to label the resulting two dimensional point clouds directly in a plot (by drawing, creating polygons, etc.).

Does anybody know of tools that can help with that?