PCA
Last updated: 2026-03-26
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Knit directory: ~/Documents/GitHub/PAINT/
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| absolute | relative |
|---|---|
| /Users/lilyheald/Documents/GitHub/PAINT/data/sgdp.wg.pca.eigenvec | data/sgdp.wg.pca.eigenvec |
| /Users/lilyheald/Documents/GitHub/PAINT/data/sgdp.wg.pca.eigenval | data/sgdp.wg.pca.eigenval |
| /Users/lilyheald/Documents/GitHub/PAINT/data/pigmentation_snps_pca.eigenvec | data/pigmentation_snps_pca.eigenvec |
| /Users/lilyheald/Documents/GitHub/PAINT/data/pigmentation_snps_pca.eigenval | data/pigmentation_snps_pca.eigenval |
| /Users/lilyheald/Documents/GitHub/PAINT/data/modern_metadata.csv | data/modern_metadata.csv |
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 05c4750 | Lily Heald | 2026-03-26 | stack snp distribution |
| html | 05c4750 | Lily Heald | 2026-03-26 | stack snp distribution |
# whole genome
colnames(eigvec_wg)[1:2] <- c("FID", "IID")
num_pcs_wg <- length(eigval_wg)
pc_names_wg <- paste0("PC", 1:num_pcs_wg)
colnames(eigvec_wg)[3:(2 + num_pcs_wg)] <- pc_names_wg
variance_explained_wg <- eigval_wg / sum(eigval_wg) * 100
pc1_label_wg <- sprintf("PC1 (%.2f%%)", variance_explained_wg[1])
pc2_label_wg <- sprintf("PC2 (%.2f%%)", variance_explained_wg[2])
pc3_label_wg <- sprintf("PC3 (%.2f%%)", variance_explained_wg[3])
pc4_label_wg <- sprintf("PC4 (%.2f%%)", variance_explained_wg[4])
# pigmentation
colnames(eigvec_pig)[1:2] <- c("FID", "IID")
num_pcs_pig <- length(eigval_pig)
pc_names_pig <- paste0("PC", 1:num_pcs_pig)
colnames(eigvec_pig)[3:(2 + num_pcs_pig)] <- pc_names_pig
variance_explained_pig <- eigval_pig / sum(eigval_pig) * 100
pc1_label_pig <- sprintf("PC1 (%.2f%%)", variance_explained_pig[1])
pc2_label_pig <- sprintf("PC2 (%.2f%%)", variance_explained_pig[2])
pc3_label_pig <- sprintf("PC3 (%.2f%%)", variance_explained_pig[3])
pc4_label_pig <- sprintf("PC4 (%.2f%%)", variance_explained_pig[3])pc_data_wg <- merge(eigvec_wg, metadata, by.x = "FID", by.y = "library_id")
ggplot(pc_data_wg, aes(x = PC1, y = PC2, color = Region)) +
geom_point(size = 3) +
geom_text(aes(label = Population_ID), vjust = -0.7, size = 3) +
labs(
title = "PCA of whole genome SNPs",
x = pc1_label_wg,
y = pc2_label_wg
) +
theme_classic(base_size = 14)
| Version | Author | Date |
|---|---|---|
| 05c4750 | Lily Heald | 2026-03-26 |
pc_data_pig <- merge(eigvec_pig, metadata, by.x = "IID", by.y = "library_id")
ggplot(pc_data_pig, aes(x = PC1, y = PC2, color = Region)) +
geom_point(size = 3) +
geom_text(aes(label = Population_ID), vjust = -0.7, size = 3) +
labs(
title = "PCA of pigmentation SNPs",
x = pc1_label_pig,
y = pc2_label_pig
) +
theme_classic(base_size = 14)
| Version | Author | Date |
|---|---|---|
| 05c4750 | Lily Heald | 2026-03-26 |
sessionInfo()R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS 26.3.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Detroit
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.4 forcats_1.0.1 dplyr_1.2.0
[4] purrr_1.2.1 readr_2.1.6 tidyr_1.3.2
[7] tibble_3.3.1 ggplot2_4.0.2 tidyverse_2.0.0
[10] stringr_1.6.0 data.table_1.18.2.1 workflowr_1.7.2
loaded via a namespace (and not attached):
[1] sass_0.4.10 generics_0.1.4 stringi_1.8.7 hms_1.1.4
[5] digest_0.6.39 magrittr_2.0.4 timechange_0.4.0 evaluate_1.0.5
[9] grid_4.4.2 RColorBrewer_1.1-3 fastmap_1.2.0 rprojroot_2.1.1
[13] jsonlite_2.0.0 processx_3.8.6 whisker_0.4.1 ps_1.9.1
[17] promises_1.5.0 httr_1.4.7 scales_1.4.0 jquerylib_0.1.4
[21] cli_3.6.5 crayon_1.5.3 rlang_1.1.7 bit64_4.6.0-1
[25] withr_3.0.2 cachem_1.1.0 yaml_2.3.12 otel_0.2.0
[29] parallel_4.4.2 tools_4.4.2 tzdb_0.5.0 httpuv_1.6.16
[33] vctrs_0.7.1 R6_2.6.1 lifecycle_1.0.5 git2r_0.36.2
[37] bit_4.6.0 fs_1.6.6 vroom_1.7.0 pkgconfig_2.0.3
[41] callr_3.7.6 pillar_1.11.1 bslib_0.10.0 later_1.4.5
[45] gtable_0.3.6 glue_1.8.0 Rcpp_1.1.1 xfun_0.56
[49] tidyselect_1.2.1 rstudioapi_0.18.0 knitr_1.51 farver_2.1.2
[53] htmltools_0.5.9 labeling_0.4.3 rmarkdown_2.30 compiler_4.4.2
[57] getPass_0.2-4 S7_0.2.1