Group

{
  allMarkdownRemark(filter: { frontmatter: { title: { ne: "" } } }) {
    group(field: frontmatter___categories) {
      fieldValue
      totalCount
      edges {
        node {
          frontmatter {
            title
          }
        }
      }
    }
    nodes {
      frontmatter {
        title
        categories
      }
    }
  }
}

You can also group values on the basis of a field e.g. the title, date or category and get the field value, the total number of occurrences and edges.

The query below gets you all categories (fieldValue) applied to a book and how many books (totalCount) a given category is applied to. In addition you are grabbing the title of books in a given category. You can see for example that there are 3 books in the magical creatures category.