Matplotlib RegularPolygon collection location on the canvas

Question

I am trying to plot a feature map (SOM) using python. To keep it simple, imagine a 2D plot where each unit is represented as an hexagon.

As it is shown on this topic

Answer 1

I've manage to find a workaround by calculating the figure size of inches according the given dpi. After, I compute the pixel distance between two adjacent points (by plotting it using a hidden scatter plot). This way I could calculate the hexagon apothem and estimate correctly the size of the hexagon's inner circle (as the matplotlib expects).

No gaps in the end!

import matplotlib.pyplot as plt
from matplotlib import colors, cm
from matplotlib.collections import RegularPolyCollection
from mpl_toolkits.axes_grid1 import make_axes_locatable
import math
import numpy as np

def plot_map(grid,
             d_matrix,
             w=1080,
            dpi=72.,
            title='SOM Hit map'):
"""
Plot hexagon map where each neuron is represented by a hexagon. The hexagon
color is given by the distance between the neurons (D-Matrix)

Args:
- grid: Grid dictionary (keys: centers, x, y ),
- d_matrix: array contaning the distances between each neuron
- w: width of the map in inches
- title: map title

Returns the Matplotlib SubAxis instance
"""
n_centers = grid['centers']
x, y = grid['x'], grid['y']
# Size of figure in inches
xinch = (x * w / y) / dpi
yinch = (y * w / x) / dpi
fig = plt.figure(figsize=(xinch, yinch), dpi=dpi)
ax = fig.add_subplot(111, aspect='equal')
# Get pixel size between to data points
xpoints = n_centers[:, 0]
ypoints = n_centers[:, 1]
ax.scatter(xpoints, ypoints, s=0.0, marker='s')
ax.axis([min(xpoints)-1., max(xpoints)+1.,
         min(ypoints)-1., max(ypoints)+1.])
xy_pixels = ax.transData.transform(np.vstack([xpoints, ypoints]).T)
xpix, ypix = xy_pixels.T

# In matplotlib, 0,0 is the lower left corner, whereas it's usually the
# upper right for most image software, so we'll flip the y-coords
width, height = fig.canvas.get_width_height()
ypix = height - ypix

# discover radius and hexagon
apothem = .9 * (xpix[1] - xpix[0]) / math.sqrt(3)
area_inner_circle = math.pi * (apothem ** 2)
collection_bg = RegularPolyCollection(
    numsides=6,  # a hexagon
    rotation=0,
    sizes=(area_inner_circle,),
    edgecolors = (0, 0, 0, 1),
    array= d_matrix,
    cmap = cm.gray,
    offsets = n_centers,
    transOffset = ax.transData,
)
ax.add_collection(collection_bg, autolim=True)

ax.axis('off')
ax.autoscale_view()
ax.set_title(title)
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="10%", pad=0.05)
plt.colorbar(collection_bg, cax=cax)

return ax