Grafeo is Matlab based program for the analysis of single-molecule localization microscopy (SMLM) data e.g., dSTORM or PALM. It works on a single molecule coordinates rather than pixelated images. Grafeo uses various pointillist approaches previously described in the literature, e.g., Voronoi Tessellation, Delaunay Triangulation, Ripley's function. The current Grafeo version is Grafeo v2.1. It has new functionalities, developed for the article: Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells, Haas et al., Science 2020. This includes the support three-colors data files, possibility to upload Nikon multicolor molecular list files, load Vutara data in '.mat' format, calculate graphs, and Ripley's function for small ROI, create different types of ROI, visualize the Z position using colormaps.