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I have a large file of functions. Each of these functions is responsible for drawing a particular part of the application. My app has x and y parameters that I use in the setup function to move the whole app around in order to try different placements. So, naturally, I need to use these x and y values to anchor each function's component rendering so that everything moves in unison if the global x,y values ever change.

My question is, is it bad practice/architecture to have these x,y values in the global namespace and having the each function directly access them like so?

function renderFace() {
   var x = App.x;
   var y = App.y;

   // drawing here
}

is there a better way i'm missing?

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...is it bad practice/architecture to have these x,y values in the global namespace... like so?

In your code, your x and y aren't in the global namespace; they're properties of App. That's a good start: you're using App.x instead of window.x.

That said, App and renderFace are coupled: you can't apply the functional behavior of renderFace to anything but the values of App.x/y. If you want to reduce coupling to make renderFace more general, it might be better to have renderFace accept x and y as arguments:

function renderFace(x, y) {
   // drawing here
}

and have some invoking code call renderFace(App.x, App.y) instead of just renderFace().

Alternatively, make your render functions actual methods of App and refer to the properties using this.

var App = {
    x: 0,
    y: 0,

    renderFace: function() {
        var x = this.x;
        var y = this.y;

        // drawing here
    }
}

By having App "own" renderFace as a method, it indicates logically that renderFace is a behavior of App.

When someone reading your code sees renderFace(), they might not know it depends on the state of App. When they see App.renderFace() or renderFace(App.x, App.y) the relationship is explicitly clear. Furthermore, by moving the identifer App out of your function, it's easy to re-use renderFace in other non-App contexts later.

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