Fix the check_data_input_order decorator

pygmt/helpers/decorators.py

@@ -857,7 +857,10 @@ def new_module(*args, **kwargs):
             New module instance that raises a warning if positional arguments
             are passed.
             """
-            if len(args) > 0:  # positional arguments are used
+            # plotting function always has the "self" parameter
+            plotting_func = 1 if len(args) > 1 and isinstance(args[0], object) else 0
+            if len(args) > 1 + plotting_func:
+                # more than one positional arguments are used
                 msg = (
                     "The function parameters has been re-ordered as 'data, x, y, [z]' "
                     f"since {deprecate_version} but you're passing positional arguments. "