Developing for Drupal 7
Using a debugger to understand which function called another one is not necessary all the time. If you look at the documentation on api.drupal.org, for example for user_load_by_name(), you will notice the documentation shows the number of 
functions calling it, which is also a link to a page listing them.



In the case of hooks, such as hook_field_info(), the documentation page shows how many functions are implementations of that hook, and the number of functions invoking that hook. 



The page listing the hook implementations can sometimes include functions that are not hook implementations; the short function description shown in that list makes evident when a function is not really a hook implementation.



In some cases, the documentation page lists the functions that reference a function, such as in the case of system_batch_page().



The documentation on api.drupal.org includes some sections that describe a group of functions correlated to each other, for example in Batch operations. The list of all the groups is on Topics.  

Other topics are linked in the API reference page.