Options for fulfilling partial orders

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Dear Shopify community,

What options exist in Shopify to handle a situation in which a customer orders an item that appears to be in stock at the time they place their order, but when we go to pick the order, we find that an item is out of stock (which could happen since we are picking stock from an active retail store.)

Depending on a variety of supply chain factors, we may prefer to back order the item and ship it later, or cancel the item and ship the balance of the order.  Is there a way to notify the customer of the situation and seek their preference, or give them the option to cancel the entire order if they so choose?

Our products often coordinate with each other, and so we can envision situations where if one item is not available, it could affect the customer's desire to have other items on their order.  We want to avoid customer dissatisfaction by providing clear and timely communication and letting our customers choose how they want their orders handled in these situations.  

What are our options and how would we handle this situation in order processing?  We are planning to use Shopify Shipping.

Thank you!