You can set PHP options you would normally set in php.ini in .user.ini.

For example, to increase the maximum filesize of uploads, create a .user.ini file (for example: ~/www/.user.ini)

upload_max_filesize = 20M
post_max_size = 25M ; post_max_size needs to be larger than upload_max_size

It is also possible to use the ini_set function, however this does not support all options.