Yes, they’re both JavaScript, you can use whichever functions are appropriate for the situation.
In this case you can just put the code in a document.ready handler, like this:
$(function() {
var canvas = document.getElementById("canvas");
if (canvas.getContext) {
var ctx = canvas.getContext("2d");
ctx.fillStyle = "rgb(200,0,0)";
ctx.fillRect (10, 10, 55, 50);
ctx.fillStyle = "rgba(0, 0, 200, 0.5)";
ctx.fillRect (30, 30, 55, 50);
}
});