Last updated: 2019-04-03
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Knit directory: Comparative_eQTL/analysis/
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genotype data from this study (as vcf-files) was merged with that from deManuel et al 2016 (after LiftOver to PanTro5) which contains 65 chimp whole-genome genotype data spanning all of 4 recognized sub-species. Snps were pruned to get variants in approximate equilibrium. Admixture algoroithm was used to examine population substructure and admixture. Results for K=4 is plotted below. See PCA of genotypes for a different look at the same set of samples based on the same set of snps.
library(plyr)
library(tidyverse)
library(knitr)
library(reshape2)
AdmixtureResults <- read.table("../output/PopulationStructure/Admixture/MergedForAdmixture.4.Q.labelled") %>%
mutate(id=paste(V1, V2)) %>%
select( fam = 1, ind=2, everything() ) %>%
select(-V3, -V4, -V5, -V6)
kable(head(AdmixtureResults))
fam | ind | V7 | V8 | V9 | V10 | id |
---|---|---|---|---|---|---|
Pan_troglodytes_ThisStudy | 549 | 1.0e-05 | 0.000010 | 0.999970 | 1e-05 | Pan_troglodytes_ThisStudy 549 |
Pan_troglodytes_ThisStudy | 570 | 1.3e-05 | 0.059266 | 0.940711 | 1e-05 | Pan_troglodytes_ThisStudy 570 |
Pan_troglodytes_ThisStudy | 389 | 1.0e-05 | 0.000010 | 0.999970 | 1e-05 | Pan_troglodytes_ThisStudy 389 |
Pan_troglodytes_ThisStudy | 456 | 1.1e-05 | 0.000010 | 0.999969 | 1e-05 | Pan_troglodytes_ThisStudy 456 |
Pan_troglodytes_ThisStudy | 623 | 1.0e-05 | 0.000010 | 0.999970 | 1e-05 | Pan_troglodytes_ThisStudy 623 |
Pan_troglodytes_ThisStudy | 438 | 1.0e-05 | 0.000010 | 0.999970 | 1e-05 | Pan_troglodytes_ThisStudy 438 |
Columns 3 to end represent admixed membership among K sub-populations.
# Reordering samples makes admixture plots prettier
AdmixtureResults$ind <- reorder(AdmixtureResults$ind, AdmixtureResults$V8)
# Rename species (fam-ID) to common name
AdmixtureResults$fam <- mapvalues(AdmixtureResults$fam, from=c("Pan_troglodytes_schweinfurthii", "Pan_troglodytes_ellioti", "Pan_troglodytes_ThisStudy", "Pan_troglodytes", "Pan_troglodytes_troglodytes", "Pan_troglodytes_verus"), to=c("Eastern", "Nigeria\nCameroon", "This Study", "Eastern", "Central", "Western"))
# plot
melt(AdmixtureResults) %>%
ggplot(aes(x = ind, y = value, fill = variable)) +
geom_bar(stat = "identity") +
scale_y_continuous(limits = c(-0.001,1.001), expand = c(0, 0)) +
facet_grid(~fam, scales="free_x", space="free_x") +
theme(legend.position="none") +
theme(axis.title.y=element_blank(), axis.title.x=element_blank(), axis.ticks.x=element_blank(), axis.text.x=element_text(size=rel(0.5), angle=70, hjust=1))
Using fam, ind, id as id variables
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] reshape2_1.4.3 knitr_1.22 forcats_0.4.0 stringr_1.4.0
[5] dplyr_0.8.0.1 purrr_0.3.2 readr_1.3.1 tidyr_0.8.2
[9] tibble_2.1.1 ggplot2_3.1.0 tidyverse_1.2.1 plyr_1.8.4
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 highr_0.8 cellranger_1.1.0 pillar_1.3.1
[5] compiler_3.5.1 git2r_0.24.0 workflowr_1.2.0 tools_3.5.1
[9] digest_0.6.18 lubridate_1.7.4 jsonlite_1.6 evaluate_0.13
[13] nlme_3.1-137 gtable_0.3.0 lattice_0.20-38 pkgconfig_2.0.2
[17] rlang_0.3.3 cli_1.1.0 rstudioapi_0.10 yaml_2.2.0
[21] haven_2.1.0 xfun_0.6 withr_2.1.2 xml2_1.2.0
[25] httr_1.4.0 hms_0.4.2 generics_0.0.2 fs_1.2.6
[29] rprojroot_1.3-2 grid_3.5.1 tidyselect_0.2.5 glue_1.3.1
[33] R6_2.4.0 readxl_1.1.0 rmarkdown_1.11 modelr_0.1.4
[37] magrittr_1.5 backports_1.1.3 scales_1.0.0 htmltools_0.3.6
[41] rvest_0.3.2 assertthat_0.2.1 colorspace_1.4-1 labeling_0.3
[45] stringi_1.4.3 lazyeval_0.2.2 munsell_0.5.0 broom_0.5.1
[49] crayon_1.3.4