Alternative view of Human Origins factors

Factor 2

This plot shows the median loading by assigned population label, with error bars capturing the 5th and 95th percentiles. Colours represent broad geographic groups. Populations in which the largest loading is less than 0.01 are not shown.

The second factor appears to capture east Asian, Oceanian and American populations, among others.

with(hoa,plot.response.by.label(factor2,Simple.Population.ID,Region))

Past versions of plot-factor-2-1.png

Factor 3

Factor 3 appears to capture mainly sub-Saharan African populations.

with(hoa,plot.response.by.label(factor3,Simple.Population.ID,Region))

Past versions of plot-factor-3-1.png

Factor 4

Factor 4 seems to capture mainly European and Middle Eastern ancestry.

with(hoa,plot.response.by.label(factor4,Simple.Population.ID,Region))

Past versions of plot-factor-4-1.png

Factor 5

Factor 5 captures Papuan and Australian populations.

with(hoa,plot.response.by.label(factor5,Simple.Population.ID,Region))

Past versions of plot-factor-5-1.png

Factor 6

Factor 6 is largely capturing South American populations.

with(hoa,plot.response.by.label(factor6,Simple.Population.ID,Region))

Past versions of plot-factor-6-1.png

Factor 7

Factor 7 seems to reflect East Asian origins.

with(hoa,plot.response.by.label(factor7,Simple.Population.ID,Region))

Past versions of plot-factor-7-1.png

Factor 8

Factor 8 is some combination of populations originating in Siberia and Russia.

with(hoa,plot.response.by.label(factor8,Simple.Population.ID,Region))

Past versions of plot-factor-8-1.png

Factor 9

Factor 9 corresponds largely to populations from India, as well as Middle Eastern and Central Eurasian groups.

with(hoa,plot.response.by.label(factor9,Simple.Population.ID,Region))

Past versions of plot-factor-9-1.png

Factor 10

Factor 10 picks up a small number groups from sub-Saharan Africa, including the Khomani and Mbuti.

with(hoa,plot.response.by.label(factor10,Simple.Population.ID,Region))

Past versions of plot-factor-10-1.png

Factor 11

Factor 11 is capturing some subset of Saharan and Middle Eastern populations.

with(hoa,plot.response.by.label(factor11,Simple.Population.ID,Region))

Factor 12

Factor 12 seems to distinguish European populations.

with(hoa,plot.response.by.label(factor12,Simple.Population.ID,Region))

Factor 13

Interpreting Factor 13 requires some better understanding of the Nganasan, Dolgan and other groups.

with(hoa,plot.response.by.label(factor13,Simple.Population.ID,Region))

Factor 14

Factor 14 is difficult to interpret.

with(hoa,plot.response.by.label(factor14,Simple.Population.ID,Region))

Factor 15

Factor 15 is also difficult to interpret.

with(hoa,plot.response.by.label(factor15,Simple.Population.ID,Region))

Factor 16

Factor 16 captures individuals of Surui origin.

with(hoa,plot.response.by.label(factor16,Simple.Population.ID,Region))

Past versions of plot-factor-16-1.png

Factor 17

Factor 17 captures the Biaka ancestral population.

with(hoa,plot.response.by.label(factor17,Simple.Population.ID,Region))

Past versions of plot-factor-17-1.png

Factor 18

Factor 18 picks out people with Karitianan origins.

with(hoa,plot.response.by.label(factor18,Simple.Population.ID,Region))

Past versions of plot-factor-18-1.png

Factor 19

Factor 19 captures the Pima ancestral population.

with(hoa,plot.response.by.label(factor19,Simple.Population.ID,Region))

Past versions of plot-factor-19-1.png

Factor 20

Factor 20 captures a small subset of central Asian populations, including Itelmen and Koryak.

with(hoa,plot.response.by.label(factor20,Simple.Population.ID,Region))

Factor 21

Factor 21 picks out the Mbuti.

with(hoa,plot.response.by.label(factor21,Simple.Population.ID,Region))

Past versions of plot-factor-21-1.png

Session information

sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] cowplot_0.9.4  ggstance_0.3.1 ggplot2_3.1.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       compiler_3.4.3   pillar_1.2.1     git2r_0.23.3    
 [5] plyr_1.8.4       workflowr_1.2.0  bindr_0.1.1      tools_3.4.3     
 [9] digest_0.6.17    evaluate_0.11    tibble_1.4.2     gtable_0.2.0    
[13] pkgconfig_2.0.2  rlang_0.3.1      yaml_2.2.0       bindrcpp_0.2.2  
[17] withr_2.1.2      stringr_1.3.1    dplyr_0.7.6      knitr_1.20      
[21] fs_1.2.6         rprojroot_1.3-2  grid_3.4.3       tidyselect_0.2.4
[25] glue_1.3.0       R6_2.2.2         rmarkdown_1.10   purrr_0.2.5     
[29] magrittr_1.5     whisker_0.3-2    backports_1.1.2  scales_0.5.0    
[33] htmltools_0.3.6  assertthat_0.2.0 colorspace_1.4-0 labeling_0.3    
[37] stringi_1.2.4    lazyeval_0.2.1   munsell_0.4.3