library
plot scan result for Novelty_resids_datarelease_07302918

Last updated: 2019-10-02

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: af8eb36

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    Untracked:  output/Proportion_matching_genotypes_after_removal_of_bad_samples.pdf
    Untracked:  output/Proportion_matching_genotypes_before_removal_of_bad_samples.pdf
    Untracked:  output/blup/
    Untracked:  output/genotype_error_marker.pdf
    Untracked:  output/genotype_frequency_marker.pdf
    Untracked:  output/m1.Novelty_resids_datarelease_07302918.RData
    Untracked:  output/m1.Novelty_resids_datarelease_07302918_coeffgeneplot.pdf
    Untracked:  output/m1.Novelty_resids_datarelease_07302918_genomescan.pdf
    Untracked:  output/m1.Novelty_residuals_RankNormal_datarelease_07302918.RData
    Untracked:  output/m1.Novelty_residuals_RankNormal_datarelease_07302918_genomescan.pdf
    Untracked:  output/m2.Novelty_resids_datarelease_07302918.RData
    Untracked:  output/m2.Novelty_resids_datarelease_07302918_genomescan.pdf
    Untracked:  output/m2.Novelty_residuals_RankNormal_datarelease_07302918.RData
    Untracked:  output/m2.Novelty_residuals_RankNormal_datarelease_07302918_genomescan.pdf
    Untracked:  output/m3.Novelty_resids_datarelease_07302918.RData
    Untracked:  output/m3.Novelty_resids_datarelease_07302918_genomescan.pdf
    Untracked:  output/m3.Novelty_residuals_RankNormal_datarelease_07302918.RData
    Untracked:  output/num.geno.pheno.in.Novelty_resids_datarelease_07302918.csv
    Untracked:  output/num.geno.pheno.in.Novelty_residuals_RankNormal_datarelease_07302918.csv
    Untracked:  output/number_crossover.pdf
    Untracked:  output/permu/
    Untracked:  output/prop_across_generation_chr_p.RData

Unstaged changes:
    Modified:   README.md
    Modified:   _workflowr.yml
    Modified:   analysis/10_qtl_permu.R
    Modified:   analysis/run_10_qtl_permu.R
    Modified:   analysis/run_11_qtl_blup.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.

This script will plot the qtl mapping results.

library

library(qtl2)
library(ggplot2)
load("data/Jackson_Lab_Bubier_MURGIGV01/gm_DO2437_qc.RData")

plot scan result for Novelty_resids_datarelease_07302918

pheno <- read.csv("data/pheno/Novelty_resids_datarelease_07302918.csv", header = TRUE)

print("m1")

[1] "m1"

load("output/m1.Novelty_resids_datarelease_07302918.RData")

#permutation results
#The default is to return the 5% significance thresholds. Thresholds for other (or for multiple) significance levels can be obtained via the alpha argument.
# operm <- list()
# for(i in 3:5){
#   operm[[i]] <- get(load(paste0("output/permu/m1_Novelty_resids_datarelease_07302918_", colnames(pheno)[14], "_", i, ".RData")))
#   operm[[i]] <- operm[[i]]$OFA.total.distance.traveled
# }
# operm <- matrix(do.call(rbind, operm[3:5]),ncol = 1)
# class(operm) <- c("scan1perm", "matrix")
# cutoff <- summary(operm, c(0.05, 0.1))[,1]

#genome-wide results
pdf(file = paste0("output/m1.Novelty_resids_datarelease_07302918", "_genomescan.pdf"), width = 14)
for(i in names(m1.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(m1.qtl.out[[i]]) # overall maximum LOD score
  plot(m1.qtl.out[[i]], gm_DO2437_qc$gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymx*1.02),
       main=i)
  # abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
  # abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
dev.off()

png 
  2

for(i in names(m1.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(m1.qtl.out[[i]]) # overall maximum LOD score
  plot(m1.qtl.out[[i]], gm_DO2437_qc$gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymx*1.02),
       main=i)
  # abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
  # abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}

#load blup results
x <- list()
for(i in colnames(pheno)[14:41]){
  y <- get(load(paste0("output/blup/m1_blup_Novelty_resids_datarelease_07302918_",i,".RData")))
  x[[i]] <- y[[i]]
}
m1.blup = x

#coeffects plot
#pdf(file = paste0("output/m1.Novelty_resids_datarelease_07302918", "_coeffgeneplot.pdf"), width = 14)
for(i in names(m1.qtl.out)){
  chr <- as.character(m1.peak[[i]][m1.peak[[i]]$lodcolumn == i,"chr"])
  par(mar=c(4.1, 4.1, 1.6, 1.6))
  plot_coefCC(m1.coef[[i]], 
              gm_DO2437_qc$gmap[chr], 
              scan1_output=m1.qtl.out[[i]], 
              bgcolor="gray95", #legend="bottomleft", 
              main =i)
  plot_coefCC(m1.blup[[i]], 
              gm_DO2437_qc$gmap[chr], 
              scan1_output=m1.qtl.out[[i]], 
              bgcolor="gray95", #legend="bottomleft", 
              main =i)
  plot(m1.snps[[i]]$lod, 
       m1.snps[[i]]$snpinfo, 
       drop_hilit=1.5, 
       genes=m1.genes[[i]],
       main = i)
}

#dev.off()


print("m2")

[1] "m2"

load("output/m2.Novelty_resids_datarelease_07302918.RData")

#permutation results
#The default is to return the 5% significance thresholds. Thresholds for other (or for multiple) significance levels can be obtained via the alpha argument.
# operm <- list()
# for(i in 3:5){
#   operm[[i]] <- get(load(paste0("output/permu/m2_Novelty_resids_datarelease_07302918_", colnames(pheno)[14], "_", i, ".RData")))
#   operm[[i]] <- operm[[i]]$OFA.total.distance.traveled
# }
# operm <- matrix(do.call(rbind, operm[3:5]),ncol = 1)
# class(operm) <- c("scan1perm", "matrix")
# cutoff <- summary(operm, c(0.05, 0.1))[,1]

#genome-wide results
pdf(file = paste0("output/m2.Novelty_resids_datarelease_07302918", "_genomescan.pdf"), width = 14)
for(i in names(m2.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(m2.qtl.out[[i]]) # overall maximum LOD score
  plot(m2.qtl.out[[i]], gm_DO2437_qc$gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymx*1.02),
       main=i)
  # abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
  # abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
dev.off()

png 
  2

for(i in names(m2.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(m2.qtl.out[[i]]) # overall maximum LOD score
  plot(m2.qtl.out[[i]], gm_DO2437_qc$gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymx*1.02),
       main=i)
  # abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
  # abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}

#load blup results
x <- list()
for(i in colnames(pheno)[14:41]){
  y <- get(load(paste0("output/blup/m2_blup_Novelty_resids_datarelease_07302918_",i,".RData")))
  x[[i]] <- y[[i]]
}
m2.blup = x

#coeffects plot
#pdf(file = paste0("output/m2.Novelty_resids_datarelease_07302918", "_coeffgeneplot.pdf"), width = 14)
for(i in names(m2.qtl.out)){
  chr <- as.character(m2.peak[[i]][m2.peak[[i]]$lodcolumn == i,"chr"])
  par(mar=c(4.1, 4.1, 1.6, 1.6))
  plot_coefCC(m2.coef[[i]], 
              gm_DO2437_qc$gmap[chr], 
              scan1_output=m2.qtl.out[[i]], 
              bgcolor="gray95", #legend="bottomleft", 
              main =i)
  plot_coefCC(m2.blup[[i]], 
              gm_DO2437_qc$gmap[chr], 
              scan1_output=m2.qtl.out[[i]], 
              bgcolor="gray95", #legend="bottomleft", 
              main =i)
  plot(m2.snps[[i]]$lod, 
       m2.snps[[i]]$snpinfo, 
       drop_hilit=1.5, 
       genes=m2.genes[[i]],
       main = i)
}

#dev.off()

print("m3")

[1] "m3"

load("output/m3.Novelty_resids_datarelease_07302918.RData")

#permutation results
#The default is to return the 5% significance thresholds. Thresholds for other (or for multiple) significance levels can be obtained via the alpha argument.
# operm <- list()
# for(i in 3:5){
#   operm[[i]] <- get(load(paste0("output/permu/m3_Novelty_resids_datarelease_07302918_", colnames(pheno)[14], "_", i, ".RData")))
#   operm[[i]] <- operm[[i]]$OFA.total.distance.traveled
# }
# operm <- matrix(do.call(rbind, operm[3:5]),ncol = 1)
# class(operm) <- c("scan1perm", "matrix")
# cutoff <- summary(operm, c(0.05, 0.1))[,1]

#genome-wide results
pdf(file = paste0("output/m3.Novelty_resids_datarelease_07302918", "_genomescan.pdf"), width = 14)
for(i in names(m3.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(m3.qtl.out[[i]]) # overall maximum LOD score
  plot(m3.qtl.out[[i]], gm_DO2437_qc$gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymx*1.02),
       main=i)
  # abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
  # abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}
dev.off()

png 
  2

for(i in names(m3.qtl.out)){
  par(mar=c(5.1, 4.1, 1.1, 1.1))
  ymx <- maxlod(m3.qtl.out[[i]]) # overall maximum LOD score
  plot(m3.qtl.out[[i]], gm_DO2437_qc$gmap, lodcolumn=1,
       col="slateblue", ylim=c(0, ymx*1.02),
       main=i)
  # abline(h=cutoff[1], col="red",lty=2) # 0.05 cutoff
  # abline(h=cutoff[2], col="red",lty=1) # 0.1 cutoff
}

#load blup results
x <- list()
for(i in colnames(pheno)[14:41]){
  y <- get(load(paste0("output/blup/m3_blup_Novelty_resids_datarelease_07302918_",i,".RData")))
  x[[i]] <- y[[i]]
}
m3.blup = x

#coeffects plot
#pdf(file = paste0("output/m3.Novelty_resids_datarelease_07302918", "_coeffgeneplot.pdf"), width = 14)
for(i in names(m3.qtl.out)){
  chr <- as.character(m3.peak[[i]][m3.peak[[i]]$lodcolumn == i,"chr"])
  par(mar=c(4.1, 4.1, 1.6, 1.6))
  plot_coefCC(m3.coef[[i]], 
              gm_DO2437_qc$gmap[chr], 
              scan1_output=m3.qtl.out[[i]], 
              bgcolor="gray95", #legend="bottomleft", 
              main =i)
  plot_coefCC(m3.blup[[i]], 
              gm_DO2437_qc$gmap[chr], 
              scan1_output=m3.qtl.out[[i]], 
              bgcolor="gray95", #legend="bottomleft", 
              main =i)
  plot(m3.snps[[i]]$lod, 
       m3.snps[[i]]$snpinfo, 
       drop_hilit=1.5, 
       genes=m3.genes[[i]],
       main = i)
}

#dev.off()

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  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   methods_3.3.2    
 [7] tools_3.3.2       digest_0.6.18     bit_1.1-14       
[10] RSQLite_2.1.1     evaluate_0.10     memoise_1.1.0    
[13] tibble_2.1.3      gtable_0.2.0      pkgconfig_2.0.1  
[16] rlang_0.4.0       DBI_1.0.0         yaml_2.2.0       
[19] parallel_3.3.2    withr_2.1.2       stringr_1.3.1    
[22] dplyr_0.8.3       knitr_1.20        fs_1.2.6         
[25] rprojroot_1.3-2   bit64_0.9-7       grid_3.3.2       
[28] tidyselect_0.2.5  glue_1.3.1        data.table_1.11.4
[31] R6_2.4.0          rmarkdown_1.11    purrr_0.3.2      
[34] blob_1.1.1        magrittr_1.5      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_qtl_mapping_Novelty_resids_datarelease_07302918

Hao He

2019-10-02

library

plot scan result for Novelty_resids_datarelease_07302918