Apple canker spreads via spores, usually transferring via wind, insects or rain and these spores infect the bark via damaged areas. I don't think it is partucularly known to infect roots so you should be ok. Bear in mind that canker tends to affect trees weakened by other factors so the soil (particularly if it is on the wet side) could still be a problem for any new tree. Personally, I'd avoid another tree in the malus family, just in case.
If you mean general planting rather than another tree, just go ahead as apple canker is species-specific.
A trowel in the hand is worth a thousand lost under a bush.
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