The spaces, which you see to the left and the right in the picture below, are called the transepts. They intersect the nave of the church and thus give the building its cruciform plan.
High on either side you see the two great St. Francis Xavier windows created by J. Morgan and Sons of Brooklyn and set in the magnificent five-light stone tracery designed by Houghton.
The design of the right window is based on a Peter Paul Rubens painting «The Miracles of St. Francis Xavier» executed in Belgium in 1621.
This is the only known copy of a Rubens work executed in stained glass. This masterpiece depicts the missionary activity of the saint in India.
With St. Francis are a novice and fellow Jesuit, Francis Marsilhas and Martim Alfonso de Sousa, Royal Governor of the Portuguese colony of Goa, along with the poor, sick and invalid to whom St. Francis so faithfully ministered.