Python - plot rectangles of known size at scatter points

Although @ralf-htp's answer is nice and clean and uses scatter, as far as I know the scale of the markers is expressed in points (see e.g. here). Moreover, if you zoom in, the custom markers will not change size.

Maybe that is just what you are looking for. If not, using separate Rectangle objects also does the trick nicely. This allows you to specify width and height in data units instead of points, and you can zoom in. If necessary, it is easy to apply a rotation as well, by setting the angle attribute:

from matplotlib import pyplot as plt
from matplotlib.patches import Rectangle

# Your data
a = ([126, 237, 116, 15, 136, 348, 227, 247, 106, 5, -96, 25, 146],
     [117, 127, 228, 107, 6, 137, 238, 16, 339, 218, 97, -4, -105])

# Your scatter plot
fig = plt.figure()
ax = fig.add_subplot(111)
ax.scatter(a[0], a[1], color = 'red', s=10)

# Add rectangles
width = 30
height = 20
for a_x, a_y in zip(*a):
    ax.add_patch(Rectangle(
        xy=(a_x-width/2, a_y-height/2) ,width=width, height=height,
        linewidth=1, color='blue', fill=False))
ax.axis('equal')
plt.show()

The result:

Note: If necessary you can obtain the Rectangle instances via ax.get_children().

you can define the markers in the verts option of matplotlib.pyplot.scatter like in Understanding matplotlib verts and https://matplotlib.org/gallery/lines_bars_and_markers/scatter_custom_symbol.html

verts : sequence of (x, y), optional

If marker is None [ this is not entirely working, cf Understanding matplotlib verts ], these vertices will be used to construct the marker. The center of the marker is located at (0, 0) in normalized units. The overall marker is rescaled by s.

source : https://matplotlib.org/api/_as_gen/matplotlib.pyplot.scatter.html

However i am not sure how to define exactly the markers you painted, you have to construct a list that contains the desired marker pixel by pixel

rectangle with verts :

verts = list(zip([-10.,10.,10.,-10],[-5.,-5.,5.,5]))
ax.scatter([0.5,1.0],[1.0,2.0], marker=(verts,0))

source : Understanding matplotlib verts