Clouds and aerosols provide unique insight into the chemical and physical processes of gas-giant planets. Mapping and characterizing the spectral features indicative of the cloud structure and composition enables an understanding of a planet's energy budget, chemistry and atmospheric dynamics1-4. Current space missions to Solar System planets produce high-quality datasets, yet the sheer amount of data obtained often prohibits detailed `by hand' analyses. Current techniques rely mainly on two approaches: identifying the existence of spectral features by dividing the fluxes of two or more spectral channels, and performing full radiative transfer calculations for individual spectra. The first method is not sufficiently accurate and the second is not easily scalable to the entire planetary surface. Here we have developed a deep learning algorithm, PlanetNet, that is able to quickly and accurately map spatial and spectral features across large, heterogeneous areas of a planet. We use PlanetNet to delineate the major components of the 2008 storm on Saturn5, enhancing the scope of the area previously studied and indicating regions that can be probed more deeply with radiative transfer models. Our spectral-component maps indicate compositional and cloud variations of the vast region affected by the storm, showing regions of vertical upwelling, and diminished clouds at the centre of compact substorms.