Last updated: 2019-03-14

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Knit directory: drift-workflow/analysis/

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Rmd d8e3da0 Peter Carbonetto 2019-03-14 Implemented function plot.response.by.label in hoa_global_alt_functions.R.
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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.

Analysis settings

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")

Set up environment

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 results

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

Factors 2–21

The following plots are intended to help interpret the factors by relating them to the provided population labels.

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))

Factor 3

Factor 4

Factor 5

Factor 6

Factor 7

Factor 8

Factor 9

Factor 10



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