We compared the changes in optical transmission spectrum induced by self-assembly on CVD graphene of (i) a model squarylium dye, namely n-butyl-squarylium dye (1,3-Bis[4-(dibutylamino)phenyl]-2,4-squaraine) and (ii) a conjugated polymer, poly(3-hexyl thiophene). We analyse the results based on Scanning Tunnelling Microscope images. The self-assembly of the zwitterionic dye is controlled by electrostatic interactions. A strong red-shift is observed and is explained in terms of electrostatic interactions with graphene. The self-assembly of polyalkylthiophenes presents a large red shift due to a strong alignment and planarization of the conjugated p-electron system and the formation of a new molecule-graphene charge-transfer exciton state.