Machine Learning to Get X, Y Coordinates From Picture of Plot
Learning means you have examples of a complex behavior and can learn the dependency of the behavior on some parameters implicitly.

In your picture, one can see the dependency rather explicitly and the dependency is rather simple: A big black disk for every sticky-note.

Solution:


Take picture data (red, green, blue and each 0..255) and for each pixel calculate total squared difference to a black disk of exactly the same diameter as the black dots in the picture (sum differences for each color). This means you compute the difference pixelwise and then square it pixelwise and then add up over the area of the disk.
Find local minima of these differences below a threshold.
The positions of these local minima are the desired positions.


Unfortunately I'm not good enough in R but I believe it can be done in a few lines if loops exist in R.