File:Four methods of dimension reduction applied to Thousand Genomes genotype data.png
From Wikimedia Commons, the free media repository
Jump to navigation
Jump to search
Size of this preview: 600 × 600 pixels. Other resolutions: 240 × 240 pixels | 480 × 480 pixels | 768 × 768 pixels | 1,024 × 1,024 pixels | 1,900 × 1,900 pixels.
Original file (1,900 × 1,900 pixels, file size: 592 KB, MIME type: image/png)
File information
Structured data
Captions
Summary
[edit]DescriptionFour 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. |
Date | |
Source | Alex Diaz-Papkovich,Luke Anderson-Trocmé,Chief Ben-Eghan,Simon Gravel https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008432 |
Author | Alex Diaz-Papkovich,Luke Anderson-Trocmé,Chief Ben-Eghan,Simon Gravel |
This file is licensed under the Creative Commons Attribution 2.5 Generic license.
|
This file was published in a Public Library of Science journal. Their website states that the content of all PLOS journals is published under the Creative Commons Attribution 4.0 license (or its previous version depending on the publication date), unless indicated otherwise.
|
Licensing
[edit]This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license.
- You are free:
- to share – to copy, distribute and transmit the work
- to remix – to adapt the work
- Under the following conditions:
- attribution – You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
- share alike – If you remix, transform, or build upon the material, you must distribute your contributions under the same or compatible license as the original.
File history
Click on a date/time to view the file as it appeared at that time.
Date/Time | Thumbnail | Dimensions | User | Comment | |
---|---|---|---|---|---|
current | 01:15, 15 June 2021 | 1,900 × 1,900 (592 KB) | Citing (talk | contribs) | Uploaded a work by Alex Diaz-Papkovich,Luke Anderson-Trocmé,Chief Ben-Eghan,Simon Gravel from Alex Diaz-Papkovich,Luke Anderson-Trocmé,Chief Ben-Eghan,Simon Gravel https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008432 with UploadWizard |
You cannot overwrite this file.
File usage on Commons
The following page uses this file:
Metadata
This file contains additional information such as Exif metadata which may have been added by the digital camera, scanner, or software program used to create or digitize it. If the file has been modified from its original state, some details such as the timestamp may not fully reflect those of the original file. The timestamp is only as accurate as the clock in the camera, and it may be completely wrong.
Horizontal resolution | 118.11 dpc |
---|---|
Vertical resolution | 118.11 dpc |
Categories:
- Genetic studies on East Asian populations
- Genetic studies on South Asian populations
- Genetic studies on Hispanic American
- Genetic studies on European populations
- Genetic studies on European Americans
- Genetic studies on African populations
- Genetic studies on African Americans
- Principal component analysis of human genetic diversity
Hidden categories: