plot scan result for conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019

Last updated: 2019-12-27

Checks: 7 0

Knit directory: csna_workflow/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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Environment: empty

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Seed: set.seed(20190918)

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Session information: recorded

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Cache: none

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File paths: relative

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Repository version: ae79216

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Rmd	45cb7a7	xhyuo	2019-10-21	13_plot_conditional_m2_qtlmapping.Rmd

plot scan result for conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019

#   This script performs plotting on qtl conditional mapping for DO mice m2, Novelty_residuals_RankNormal_datarelease_12182019
library(qtl2)
library(ggplot2)
load("data/Jackson_Lab_11_batches/gm_DO2816_qc.RData")
pheno <- read.csv("data/pheno/Novelty_residuals_RankNormal_datarelease_12182019.csv", header = TRUE)

print("m2")

[1] "m2"

load("output/condi.m2.qtl.out.RData")

#genome-wide results
pdf(file = paste0("output/conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019", "_genomescan.pdf"), width = 14)
for(i in names(condi.m2.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(condi.m2.qtl.out[[i]]) # overall maximum LOD score
  plot(condi.m2.qtl.out[[i]], gm_DO2816_qc$gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymx*1.02),
       main=i)
}
dev.off()

png 
  2

for(i in names(condi.m2.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(condi.m2.qtl.out[[i]]) # overall maximum LOD score
  plot(condi.m2.qtl.out[[i]], gm_DO2816_qc$gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymx*1.02),
       main=i)
}

sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_3.1.0 qtl2_0.18    

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2        pillar_1.3.1      git2r_0.23.0     
 [4] plyr_1.8.4        workflowr_1.4.0   tools_3.3.2      
 [7] digest_0.6.18     bit_1.1-14        RSQLite_2.1.1    
[10] evaluate_0.10     memoise_1.1.0     tibble_2.1.3     
[13] gtable_0.2.0      pkgconfig_2.0.1   rlang_0.4.0      
[16] DBI_1.0.0         yaml_2.2.0        parallel_3.3.2   
[19] withr_2.1.2       stringr_1.3.1     dplyr_0.8.3      
[22] knitr_1.20        fs_1.2.6          rprojroot_1.3-2  
[25] bit64_0.9-7       grid_3.3.2        tidyselect_0.2.5 
[28] glue_1.3.1        data.table_1.11.4 R6_2.4.0         
[31] rmarkdown_1.11    purrr_0.3.2       blob_1.1.1       
[34] magrittr_1.5      whisker_0.3-2     backports_1.1.2  
[37] scales_1.0.0      htmltools_0.3.6   assertthat_0.2.1 
[40] colorspace_1.4-0  stringi_1.2.4     lazyeval_0.2.1   
[43] munsell_0.5.0     crayon_1.3.4

plot_conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019

Hao He

2019-12-27

plot scan result for conditional_m2.Novelty_residuals_RankNormal_datarelease_12182019