In July 1844, while engaging armed rioters in Southwark, Pennsylvania, he was wounded by a musket ball to the left groin.

Apparently influenced by Robert Hunt's research into the effect of different wavelengths of light on the growth of plants,[5][6]: 214–215  in his later years, Gen. Pleasonton came to a theory that the blue wavelengths from the sun are inherently unique and that the blue rays from the sun are especially influential in the growth of plant and animal life.

Between the years 1861 and 1876, he tested this theory by establishing greenhouses to grow grapes and ran experiments on plants and animals.

In 1871 Pleasonton published his findings in a monograph entitled On the Influence of the Blue Color of the Sky in developing Animal and Vegetable Life.

After continuing his experiments and expanding his theories, in 1876 he published his main work, the book The Influence of the Blue Ray of the Sunlight and of the Blue Color of the Sky: In developing animal and vegetable life; in arresting disease, and in restoring health in acute and chronic disorders to human and domestic animals.

Pleasonton's theory led to what was called the "Blue-glass Craze", whereby people began growing crops under blue light.

Edwin Dwight Babbitt was also influenced by this concept and published a book about chromotherapy in 1878, entitled The Principles of Light and Color.