What clues hint that the mysterious lodger at the Admiral Benbow is a pirate?

The mysterious lodger talks about the sea, hides from seafarers, tells terrifying stories of life at sea, drinks a lot, and owns a great sea chest, which he guards with his life.

I followed him in, and I remember observing the contrast the neat, bright doctor, with his powder as white as snow and his bright, black eyes and pleasant manners, made with the coltish country folk, and above all, with that filthy, heavy, bleared scarecrow of a pirate of ours, sitting, far gone in rum, with his arms on the table. Suddenly he—the captain, that is—began to pipe up his eternal song:

At first I had supposed "the dead man's chest" to be that identical big box of his upstairs in the front room, and the thought had been mingled in my nightmares with that of the one-legged seafaring man. But by this time we had all long ceased to pay any particular notice to the song; it was new, that night, to nobody but Dr. Livesey, and on him I observed it did not produce an agreeable effect, for he looked up for a moment quite angrily before he went on with his talk to old Taylor, the gardener, on a new cure for the rheumatics.