This is pretty trivial, but Google came up with no viable results so I had to do research. With a TI83/84, you simply scroll over the y’s = sign and toggle it on or off. There is no toggle with the TI89 though.
Looking at the graphing screen doesn’t help a lot. It’s impossible to get to the check by the enabled functions. The options above the interactive window are also mostly useless. Except for F4. That button, when hovering over a function, will toggle it’s graphing.
To see it in action, try entering x into y1. Then hit star and the F3 key. You’ll see your graph. Then go back using star F1 and move the cursor to y1. Hit F4 while selected and you’ll notice the check mark by the function go away. If you run the graph again, it won’t be visible because you turned it off.
Happy graphing.