# Overwrite points from pcolormesh if they aren't contained in a polygon

A turtle’s shape is stored in its shape variable and can be set using the set command,,Example: you can change any turtle from it’s existing NetLogo color to a half transparent version of that color using:,You can also define new turtle, patch and link variables using the turtles-own, patches-own and links-own keywords, like this:,Turtles, links, and labels can all contain RGBA lists as their color variables, however, patches cannot have RGBA pcolors You can set the color of a turtle to be approximately half transparent pure red with the following code:

`ask one - of turtles[set color green]`

`ask one - of patches[sprout 1]`

Here is a possible fix, It requires that the projection doesn't change int he life of the pcolormesh

```
import numpy as np
def _interp_grid(X):
# helper
for below
if np.shape(X)[1] > 1:
dX = np.diff(X, axis = 1) / 2.
X = np.hstack((X[: , [0]] - dX[: , [0]],
X[: ,: -1] + dX,
X[: , [-1]] + dX[: , [-1]]))
return X
x = np.array([1, 2, 0])
y = np.array([1, 2])
X, Y = np.meshgrid(x, y)
_interp_grid(X)
```

If X and/or Y are 1-D arrays or column vectors they will be expanded as needed into the appropriate 2-D arrays, making a rectangular grid,,C may be a masked array

`pcolor([X, Y, ] C, ** kwargs)`

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import geopandas as gpd import matplotlib.pyplot as plt import numpy as np import matplotlib as mpl from shapely.geometry import Point # Load polygon world = gpd.read_file(gpd.datasets.get_path("naturalearth_lowres")) UK = world[world.iso_a3 == "GBR"] # plot 1 #UK.boundary.plot() # Simulate a spatial pattern xlims = (-8, 3) ylims = (49, 60) resolution = 0.05 # 0.05 # slice() y, x = np.mgrid[slice(ylims[0], ylims[1] + resolution, resolution), slice(xlims[0], xlims[1] + resolution, resolution)] z = 0.5 * x + np.sin(x) ** 2 + np.cos(y) # Target geometry, for point inside / outside polygon operation ukgeom = UK['geometry'].values[0] def prep_z(Xs, Ys, Zs): # Xs, Ys: result of np.meshgrid(lon, lat) # Zs: function of (Xs, Ys) to be manipulated; here hard - coded as `new_z` for ro, (arow, acol) in enumerate(zip(Xs, Ys)): # need 2 level loop to handle each grid point for co, xiyi in enumerate(zip(arow, acol)): pnt1 = Point(xiyi) if pnt1.within(ukgeom): new_z[ro][co] = 1 #0:white, 1:black with cm= 'binary' else : new_z[ro][co] = 0 pass pass # Usage of the function above: prep_z(x, y, z) # Result: new_z is modified. # New z for locations in /outside-polygon operation new_z = np.zeros(z.shape) prep_z(x, y, z) # create custom colormap to use later new_binary = mpl.colors.ListedColormap(np.array([ [1., 1., 1., 1.], [0., 0., 0., 0.] ])) # 0: white, 1: transparent with cm = 'new_binary' # do not use alpha option to get the intended result # Plot 2 fig, ax = plt.subplots(figsize = (6, 10)) im = ax.pcolormesh(x, y, z, cmap = 'viridis', zorder = 1) im2 = ax.pcolormesh(x, y, new_z, cmap = new_binary, zorder = 2) # do not use alpha to get transparent mask UK.boundary.plot(ax = ax, color = 'black', zorder = 10) fig.colorbar(im, ax = ax, shrink = 0.5) plt.show()

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