What axis does temperature go on?

Whichever axis you like. To some extent it depends on whether temperature is the independent or the dependent variable.

If the graph is of the temperature of some food when it has been in an over for different lengths of time, then the independent variable is the time and the temperature should be on the vertical axis. However, if the graph is of the temperature of the same food and the number of bacteria present in it, then the temperature is the independent variable and should be on the horizontal axis.