PH TO CANDA WITH LAYOVER IN JAPAN

Hello, I am a first time flyer, from the Philippines. I have an immigrant visa and I will be flying to Canada in a few months. This is my itinerary:

MANILA TO TOKYO HANEDA (JAPAN AIRLINES) TOKYO HANEDA TO TORONTO (AIR CANADA)

I am just confused because I will be riding in different airlines, my question is I will be getting my baggages on my final destination or do I have to re-check in my baggages when I arrived in Japan and go through immigration, security, and such again???

more info:

• I have a layover for 13 hours (4am to 6pm)
• will be departing in the same terminal as my arrival terminal
• purchase ONE TICKET only

Thank you so much in advance!