Interplay between the spatial pattern of selective environment, the mode of directional selection, and the pattern of migration is expected to determine how beneficial alleles propagate over geographic regions. With the availability of whole-genome sequencing data from hundreds of wild-derived individuals in African populations of Drosophila melanogaster and the method of detecting loci under ongoing directional selection, it is now feasible to investigate the general mode and spatial patterns of positive directional selection. We scanned for signatures of incomplete selective sweeps in Rwanda and Zambia samples of D. melanogaster using our recently developed composite likelihood ratio (CLR) method and a haplotype homozygosity method (nSL test). By choosing only significant signals detected by either one or both tests and re-examining the local topology of genealogical trees, we selected 46 loci with clear patterns of incomplete sweep for further analysis. The geographical distribution of the putatively beneficial haplotype at each locus was then obtained from a genealogical tree constructed for all individuals from 11 populations across Africa. We observed distinct spatial distributions of beneficial haplotype across loci, suggesting the operation of different modes of positive selection. To explain this range of results, simulations were performed under the island model of two subpopulations with selective pressure that vary in space (local vs. global selection) and time (constant vs. diminishing selection). More than half of the loci appear to be under simple selection with constant selective pressure. However, there are also many loci compatible with diminishing selection, for example due to heterozygous advantage. We also found a few loci under incomplete soft selective sweeps. One of them is characterized by a complex haplotype distribution that can only be explained by very high adaptive mutation rate and possibly heterozygous advantage.