Last updated: 2019-03-14
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Knit directory: drift-workflow/analysis/
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | 7643dfb | Peter Carbonetto | 2019-03-14 | wflow_publish(“hoa_global_alt.Rmd”) |
Rmd | f703ecd | Peter Carbonetto | 2019-03-14 | wflow_publish(“hoa_global_alt.Rmd”) |
Rmd | d484e71 | Peter Carbonetto | 2019-03-14 | wflow_publish(“hoa_global_alt.Rmd”) |
Rmd | 0d9dd25 | Peter Carbonetto | 2019-03-14 | wflow_publish(“hoa_global_alt.Rmd”) |
html | 749f46a | Peter Carbonetto | 2019-03-14 | Fixed some of the factor plots in hoa_global_alt page. |
Rmd | 862414e | Peter Carbonetto | 2019-03-14 | wflow_publish(“hoa_global_alt.Rmd”) |
html | 93a1bec | Peter Carbonetto | 2019-03-14 | Added more factor plots to hoa_global_alt analysis. |
Rmd | abb7bcc | Peter Carbonetto | 2019-03-14 | wflow_publish(“hoa_global_alt.Rmd”) |
html | cf9ecd9 | Peter Carbonetto | 2019-03-14 | Added first factor plot to hoa_global_alt page. |
Rmd | 54d183a | Peter Carbonetto | 2019-03-14 | Added description of factor 2 to hoa_global_alt.Rmd. |
html | 54d183a | Peter Carbonetto | 2019-03-14 | Added description of factor 2 to hoa_global_alt.Rmd. |
Rmd | d8e3da0 | Peter Carbonetto | 2019-03-14 | Implemented function plot.response.by.label in hoa_global_alt_functions.R. |
html | 2f78a1d | Peter Carbonetto | 2019-03-14 | Created initial rendering of hoa_global_alt analysis. |
Rmd | a749d22 | Peter Carbonetto | 2019-03-14 | wflow_publish(“hoa_global_alt.Rmd”, verbose = TRUE) |
Rmd | fdf11c4 | Peter Carbonetto | 2019-03-14 | Added hoa_global_alt_functions.R. |
Rmd | 9c2be6a | Peter Carbonetto | 2019-03-14 | Added hoa_global_alt.Rmd. |
Following from the initial analysis, this analysis presents an alternative view of the factors.
This is the file with a large data frame containing the factor loadings and other sample information.
loadings.file <- file.path("..","sandbox","loadings-forpeter-03-12-2019.rds")
Load several R packages and function definitions used in the code chunks below.
library(ggplot2)
library(ggstance)
library(cowplot)
source(file.path("..","code","hoa_global_alt_functions.R"))
Load the data frame containing the factor loadings and population labels.
hoa <- load.results(loadings.file)
This data frame should contain information on 2,018 genotype samples:
nrow(hoa)
[1] 2018
The following plots are intended to help interpret the factors by relating them to the provided population labels.
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))
Version | Author | Date |
---|---|---|
cf9ecd9 | Peter Carbonetto | 2019-03-14 |
Factor 3 appears to capture mainly sub-Saharan African populations.
with(hoa,plot.response.by.label(factor3,Simple.Population.ID,Region))
Factor 4 seems to capture mainly European and Middle Eastern ancestry.
with(hoa,plot.response.by.label(factor4,Simple.Population.ID,Region))
Factor 5 captures Papuan and Australian populations.
with(hoa,plot.response.by.label(factor5,Simple.Population.ID,Region))
Factor 6 is largely capturing South American populations.
with(hoa,plot.response.by.label(factor6,Simple.Population.ID,Region))
Factor 7 seems to reflect East Asian origins.
with(hoa,plot.response.by.label(factor7,Simple.Population.ID,Region))
Factor 8 is some combination of populations originating in Siberia and Russia.
with(hoa,plot.response.by.label(factor8,Simple.Population.ID,Region))
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))
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))
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 seems to distinguish European populations.
with(hoa,plot.response.by.label(factor12,Simple.Population.ID,Region))
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 is difficult to interpret.
with(hoa,plot.response.by.label(factor14,Simple.Population.ID,Region))
Factor 15 is also difficult to interpret.
with(hoa,plot.response.by.label(factor15,Simple.Population.ID,Region))
Factor 16 captures individuals of Surui origin.
with(hoa,plot.response.by.label(factor16,Simple.Population.ID,Region))
Factor 17 captures the Biaka ancestral population.
with(hoa,plot.response.by.label(factor17,Simple.Population.ID,Region))
Factor 18 picks out people with Karitianan origins.
with(hoa,plot.response.by.label(factor18,Simple.Population.ID,Region))
Factor 19 captures the Pima ancestral population.
with(hoa,plot.response.by.label(factor19,Simple.Population.ID,Region))
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 picks out the Mbuti.
with(hoa,plot.response.by.label(factor21,Simple.Population.ID,Region))
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