I'm not sure if this is the best way, but you set the level on org.apache.logging.log4j.core.config.LoggerConfig which you can get from the LoggerContext via the LogManager.
Once set, you can update the loggers with the new configuration.
As an example:
public static void main(String[] args) {
Logger log = LogManager.getLogger(LogManager.ROOT_LOGGER_NAME);
log.error("An error");
log.debug("A debug");
LoggerContext ctx = (LoggerContext) LogManager.getContext(false);
Configuration conf = ctx.getConfiguration();
conf.getLoggerConfig(LogManager.ROOT_LOGGER_NAME).setLevel(Level.DEBUG);
ctx.updateLoggers(conf);
log.error("Another error");
log.debug("Another debug");
}
Yields:
14:03:41.346 [main] ERROR - An error
14:03:41.348 [main] ERROR - Another error
14:03:41.348 [main] DEBUG - Another debug
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