Subcellular chemical heterogeneity plays a key role in cell organization and function. However the biomechanics underlying the structure-function relationship is governed by cell substructures which are poorly resolved using conventional chemical imaging methods. To date, advances in sub-diffraction limited infrared (IR) nanoscopy have permitted intracellular chemical mapping. In this work we report how image analysis applied to a combination of IR absorption nanoimaging and topographic data permits quantification of chemical complexity at the nanoscale, enabling the analysis of biochemical heterogeneity in mammalian cancer cells on the scale of subcellular features.