How to modify the query that the views integration with the chart API module provides? I am using Google Charts API module to generate a pie chart of a content type with the fields Blood-group and count representing the sectors.

For this I need to completely alter the query (= select from a different table) that the views integration provides.

My question: Can I use hook_views_query_alter?
To create charts in Drupal, there are plenty of modules available. Refer to the comparison of charting modules for an overview. After doing so, it should be clear that the names (and namespaces) of various charting modules are pretty confusing. Therefor I suggest you add a link to the exact 'Google Charts API' module this question is about.

Moreover, if I correctly understand the question, it seems to me that this is a rather straight forward requirement that can be easily addressed with (at least) the Charts module, i.e. the views integration of it (provides a new views style plugin to transform tabular view results into a chart). I recently created quite a lot of new Charts documentation that should help to get started with it.

The Charts module ships with out-of-the-box samples which are straight forward to adapt to fit your needs, e.g. by cloning these samples in a new views display or a new view. Of course there are other alternatives in that comparison that might be a better fit for this specific case.

Be aware: I'm a new (co-) maintainer of both Chart and Charts (confusing module names, I didn't invent them), and the author of the comparison of charting modules.