File:Four methods of dimension reduction applied to Thousand Genomes genotype data.png

English: (A) PCA maps individuals in a triangle with vertices corresponding to African, Asian, and European continental ancestry. Discarding lower-variance PCs leads to overlap of populations with no close affinity, such as Central and South American populations with South Asians. (B) t-SNE forms groups corresponding to continents, with some overlap between European and Central and South American people. Smaller subgroups are visible within continental clusters. The cloud of peripheral points results from the method’s poor convergence. (C) UMAP forms distinct clusters related to continent with clearly defined subgroups. Japanese, Finnish, Luhya, and some Punjabi and Telugu populations form separate clusters consistent with their population history. (D) UMAP on the first 15 principal components forms fine-scale clusters for individual populations. Groups closely related by ancestry or geography, such as African Caribbean/African American, Spanish/Italian, and Kinh/Dai populations cluster together. Axes in UMAP and t-SNE are arbitrary. Since the algorithms prioritize local distances, long distances between clusters are not meaningful. ACB, African Caribbean in Barbados; ASW, African Ancestry in Southwest US; BEB, Bengali; CDX, Chinese Dai; CEU, Utah residents with Northern/Western European ancestry; CHB, Han Chinese; CHS, Southern Han Chinese; CLM, Colombian in Medellin, Colombia; ESN, Esan in Nigeria; FIN, Finnish; GBR, British in England and Scotland; GWD, Gambian; GTH, Gujarati; IBS, Iberian in Spain; ITU, Indian Telugu in the UK; JPT, Japanese; KHV, Kinh in Vietnam; LWK, Luhya in Kenya; MSL, Mende in Sierra Leone; MXL, Mexican in Los Angeles, California; PEL, Peruvian; PJL, Punjabi in Lahore, Pakistan; PUR, Puerto Rican; STU, Sri Lankan Tamil in the UK; TSI, Toscani in Italy; YRI, Yoruba in Nigeria.