I am the rose of Sharon, and the lily of the valley.
~ The Song of Solomon 2:1
Flowers are often used as visual metaphors in the Christian Tradition. In antiquity, the white lily was interpreted as a symbol for purity and, thus, became associated with the Virgin Mary. The red rose was interpreted as a symbol for the martyrdom of the saints under the persecution from Rome. These two flowers also became associated with the purity and sacrifice of Jesus. Often, red roses will adorn the Altar on Good Friday, followed by white lilies on the Altar for Easter. So in addition to symbolizing purity, the white lily - in particular the fleurs-de-lys - became a symbol for the victorious Christ. In the windows in the Nave (the area for congregational seating) of Ionia First, all of the symbols refer to Jesus Christ. It is probable, therefore, that the intention of the artist was to associate the purity and holiness of Jesus with his sacrifice on the Cross. This makes a pointed theological statement: true purity leads to sacrifice. We understand that the source of Christ's purity is the eternal love of God. The love of the Son of God for the creation which has come into being through him leads to his taking the suffering of the world into himself. The white is stained with red. For me, the two flowers together point to the profound mystery of the Cross: "For our sake he made him to be sin who knew no sin, so that in him we might become the righteousness of God" (2 Cor. 5:21).
Source: Ferguson, George. Signs and Symbols in Christian Art (Oxford: 1961).