Last updated: 2023-07-11

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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