Covariance Correlations
Last updated: 2023-07-11
Checks: 6 1
Knit directory: dgrp-starve/
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| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/mr.mash_f_sr.top3.Rds | snake/data/22_cov/genetic/mr.mash_f_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/multigblup_f_sr.top3.Rds | snake/data/22_cov/genetic/multigblup_f_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/multibayesC_f_sr.top3.Rds | snake/data/22_cov/genetic/multibayesC_f_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/mr.mash_f_sr.top3.Rds | snake/data/22_cov/residual/mr.mash_f_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/multigblup_f_sr.top3.Rds | snake/data/22_cov/residual/multigblup_f_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/multibayesC_f_sr.top3.Rds | snake/data/22_cov/residual/multibayesC_f_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/mr.mash_m_sr.top3.Rds | snake/data/22_cov/genetic/mr.mash_m_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/multigblup_m_sr.top3.Rds | snake/data/22_cov/genetic/multigblup_m_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/multibayesC_m_sr.top3.Rds | snake/data/22_cov/genetic/multibayesC_m_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/mr.mash_m_sr.top3.Rds | snake/data/22_cov/residual/mr.mash_m_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/multigblup_m_sr.top3.Rds | snake/data/22_cov/residual/multigblup_m_sr.top3.Rds |
| /data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/multibayesC_m_sr.top3.Rds | snake/data/22_cov/residual/multibayesC_m_sr.top3.Rds |
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| Rmd | 3d215b2 | nklimko | 2023-07-11 | added ggcorrplot2 |
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Methods
Mr. Mash
GBLUP
BayesC
Code
Female
Genetic Correlation
traits <- c('starvation','cafe','free.glycerol','free.glucose')
covMash <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/mr.mash_f_sr.top3.Rds")
covBlup <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/multigblup_f_sr.top3.Rds")
covBayes <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/multibayesC_f_sr.top3.Rds")
allCor <- list(mr.mash=covMash, gblup=covBlup, bayesC=covBayes)
#corrPlots----
j <- 1
for(i in allCor){
rownames(i) <- traits
colnames(i) <- traits
gg[[j]] <- ggcorrplot(i, lab=1)
j <- j + 1
}Residual Correlation
covMash <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/mr.mash_f_sr.top3.Rds")
covBlup <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/multigblup_f_sr.top3.Rds")
covBayes <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/multibayesC_f_sr.top3.Rds")
allCor <- list(mr.mash=covMash, gblup=covBlup, bayesC=covBayes)
#corrPlots----
for(i in allCor){
rownames(i) <- traits
colnames(i) <- traits
gg[[j]] <- ggcorrplot(i, lab=1)
j <- j + 1
}Male
Genetic Correlation
covMash <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/mr.mash_m_sr.top3.Rds")
covBlup <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/multigblup_m_sr.top3.Rds")
covBayes <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/genetic/multibayesC_m_sr.top3.Rds")
allCor <- list(mr.mash=covMash, gblup=covBlup, bayesC=covBayes)
#corrPlots----
for(i in allCor){
rownames(i) <- traits
colnames(i) <- traits
gg[[j]] <- ggcorrplot(i, lab=1)
j <- j + 1
}Residual Correlation
covMash <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/mr.mash_m_sr.top3.Rds")
covBlup <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/multigblup_m_sr.top3.Rds")
covBayes <- readRDS("/data2/morgante_lab/nklimko/rep/dgrp-starve/snake/data/22_cov/residual/multibayesC_m_sr.top3.Rds")
allCor <- list(mr.mash=covMash, gblup=covBlup, bayesC=covBayes)
#corrPlots----
for(i in allCor){
rownames(i) <- traits
colnames(i) <- traits
gg[[j]] <- ggcorrplot(i, lab=1)
j <- j + 1
}Female: Genetic and Residual Correlations
mr.mash
plot_grid(gg[[1]],gg[[4]], ncol=2)
gblup
plot_grid(gg[[2]],gg[[5]], ncol=2)
bayesC
plot_grid(gg[[3]],gg[[6]], ncol=2)
Male: Genetic and Residual Correlations
mr.mash
plot_grid(gg[[7]],gg[[10]], ncol=2)
gblup
plot_grid(gg[[8]],gg[[11]], ncol=2)
bayesC
plot_grid(gg[[9]],gg[[12]], ncol=2)
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.5 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /opt/ohpc/pub/libs/gnu9/openblas/0.3.7/lib/libopenblasp-r0.3.7.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggcorrplot_0.1.4 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[5] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[9] tidyverse_2.0.0 scales_1.2.1 viridis_0.6.2 viridisLite_0.4.2
[13] doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2 qqman_0.1.8
[17] cowplot_1.1.1 ggplot2_3.4.2 data.table_1.14.8 dplyr_1.1.2
[21] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 getPass_0.2-2 ps_1.7.2 rprojroot_2.0.3
[5] digest_0.6.31 utf8_1.2.3 plyr_1.8.8 R6_2.5.1
[9] evaluate_0.20 httr_1.4.5 highr_0.10 pillar_1.9.0
[13] rlang_1.1.1 rstudioapi_0.14 whisker_0.4.1 callr_3.7.3
[17] jquerylib_0.1.4 rmarkdown_2.20 labeling_0.4.2 munsell_0.5.0
[21] compiler_4.1.2 httpuv_1.6.9 xfun_0.37 pkgconfig_2.0.3
[25] htmltools_0.5.4 tidyselect_1.2.0 gridExtra_2.3 codetools_0.2-19
[29] fansi_1.0.4 calibrate_1.7.7 tzdb_0.3.0 withr_2.5.0
[33] later_1.3.0 MASS_7.3-58.3 grid_4.1.2 jsonlite_1.8.4
[37] gtable_0.3.3 lifecycle_1.0.3 git2r_0.31.0 magrittr_2.0.3
[41] cli_3.6.1 stringi_1.7.12 cachem_1.0.7 farver_2.1.1
[45] reshape2_1.4.4 fs_1.6.1 promises_1.2.0.1 bslib_0.4.2
[49] generics_0.1.3 vctrs_0.6.2 tools_4.1.2 glue_1.6.2
[53] hms_1.1.3 processx_3.8.0 fastmap_1.1.1 yaml_2.3.7
[57] timechange_0.2.0 colorspace_2.1-0 knitr_1.42 sass_0.4.5