Lines 3 to 34 have a lot of unrelated concepts that are all grouped together. Contained in this section are things like:

• global state which the app mutates as it runs (mouse position, the dots themselves, the width and height of the canvas)
• immutable constants (the array of possible colors for the dots)
• elements queried from the DOM (the canvas)
• bootstrapping code for the canvas API (canvas.getContext("2d"))
• bootstrapping code for event listeners (mousemove, mousedown)

Grouping all of these unrelated concepts together is going to confuse a first-time reader of the code. A newcomer to the file will be able to parse it more quickly if these discrete concepts are organized into groupings within the file, e.g.:

// constants
colors = [
"#af0",
// etc
];

// DOM elements
const canvas = document.getElementById("canvas")

// state
let mouse = { x: 0, y: 0 } 
const dotsHolder = []
canvas.height = window.innerHeight;
canvas.width = window.innerWidth;

It looks like this requestAnimationFrame polyfill is something that was copy/pasted from Stack Overflow or a gist or elsewhere.

Nothing wrong with that of course! If it works it works, and major bonus points for keeping cross-browser compatibility in mind. But I'd advise a couple of things:

• define this as a proper named function at the top of the file instead of defining and calling it within an IIFE. Functionally, the result will be the same, but by putting it at the top of the file and calling the function along with your init code, you make it easier to ignore. It doesn't have anything to do with the logic of the app, so it shouldn't be situated within the app code itself.
• arrow functions instead of function keyword-defined functions to cut down on verbosity
• and, if you've got the same tendency for code gardening as I do, I'd suggest doing some light gardening and modernizing of the code, e.g.: let instead of var. Once again, no functional changes will result, but you'll have a tidier garden, and future maintainers will want to keep the garden tidy if they see that others have put in an effort to be neat and conscientious.

Putting a little whitespace between mouse.y = ... and if (mouseMove) will make this just a little bit more readable. This gets back to the idea of grouping like-things together: updating the mouse x and y positions and drawing a line on the canvas are both things that happen on mousemove, but are nevertheless separate actions. Giving a little breathing room between these two actions will aide comprehension for newcomers to the code.

Lines 65 to 88 should be grouped together with the other setup code above. This will help distinguish between the setup code and the real meat of the app (the code that draws and animates the dots themselves), and grouping like-things together will aid in reading comprehension for others.

I'd suggest writing this as a makeDot function which returns a simple object when called rather than defining your dots as classes:

• As it is, you're using this class to fill the dotsHolder array by creating new instances of the dot class within a for loop, which is a functional programming-flavored technique as it is.
• The class doesn't contain any state (all of the mutable state in the app, most notably dotsHolder, is defined with global variables already), so you don't get the benefit of treating a class as a stateful object either.
• And because it's written as a class, you're encouraged to write things like dots.draw as prototype functions on the class itself. This couples dots.draw to the dots class, and can make it difficult in the future to decouple them if needed. Pure functions which aren't tied to a particular class are more portable and easier to adapt to new scenarios as they arise.

So! I'd suggest ditching the class and going with something like this instead:

const makeDot = () => {
const radius = Math.random() * 10;

return {
xPos: Math.random() * canvas.width,
yPos: Math.random() * canvas.height,
radius: radius,
vx: Math.cos(radius),
vy: Math.sin(radius),
// etc
};
}

const drawDots = dot => {
// dot drawing code
}