how to plot with color according to factor keeping a fixed number of levels?

On Sun, 31 Jul 2022 15:26:14 +0200

but since there is no Y==0, the colors are shifted because Z has only
two levels.

You're almost there: you're already making Z a factor. Use factor(Z,
levels = c(-1, 0, 1)) to make a factor with a predefined range of
values.

Best regards,
Ivan