If the axis on your mouse screws up like mine did, you can move it left-right and see the counter-clockwise rotation required to make it horizontal, then up-down and see that rotation (degrees) then pass those to this script to get a linux cmd which will transform it accordingly.

transform_mouse_coords

#!/usr/bin/python3.7
from math import sin, cos, pi
import subprocess
import sys
skew_x_axis=int(sys.argv[1])
skew_y_axis=int(sys.argv[2])  # if when you move your mouse up it moves up and to the right leaving 10 degrees drift from the y axis, write 10 here
c=pi/180.


def get_rotation_matrix(xt, yt):
  return '%5f %.5f 0.00000 %5f %.5f 0.00000 0.00000 0.00000 1.00000' % (cos(c*xt), sin(c*yt), -sin(c*xt), cos(c*yt))


def get_device_name():
  xinput_list = subprocess.check_output('xinput list', shell=True).decode('utf').split('\n')
  mice = [line for line in xinput_list if 'Mouse' in line]
  if len(mice) == 0:
    print("Could not find a mouse in the xinput list, modify this method to return the relevant id from the following:", output)
    raise(ValueError("This program will exit now"))
  if len(mice)>1:
    print("WARNING: You seem to have multiple mice. You'll need to pick the relevant id. We'll just take the first one we found though.")
  dname = mice[0].split('id=')[1].split()[0]
  device_name = int(dname)
  return device_name


transformed_coords = get_rotation_matrix(skew_x_axis, skew_y_axis)

device_name = get_device_name()

cmd=f"xinput set-prop '{device_name}' 'Coordinate Transformation Matrix' {transformed_coords}"
print(cmd)
if 'y' in input('ok? ').lower():
  subprocess.check_output(cmd, shell=True)